dbSNP rs2955587: FAM86B3P:n.904+3282A>G (chr8-8240557-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000522393.1(FAM85B):n.302-8T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 1,588,812 control chromosomes in the GnomAD database, including 168,559 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.39 ( 14144 hom., cov: 33)

Exomes 𝑓: 0.45 ( 154415 hom. )

Consequence

FAM85B
ENST00000522393.1 splice_region, intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0370

Publications

12 publications found

Variant links:

Genes affected

FAM86B3P (HGNC:):

FAM86B3P links:

ALG1L13P (HGNC:44382): (ALG1 like 13, pseudogene)

ALG1L13P links:

FAM85B (HGNC:32160): (family with sequence similarity 85 member B)

FAM85B links:

FAM86B3P (HGNC:44371): (family with sequence similarity 86 member B3, pseudogene)

FAM86B3P links:

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new If you want to explore the variant's impact on the transcript ENST00000522393.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522393.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM86B3P	NR_024361.1		n.929+3282A>G		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
FAM86B3P	ENST00000522601.5	TSL:1	n.904+3282A>G	intron	N/A
FAM86B3P	ENST00000310542.3	TSL:2	n.189A>G	non_coding_transcript_exon	Exon 1 of 2
ALG1L13P	ENST00000519320.1	TSL:6	n.117-9T>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.387

AC:

58820

AN:

151940

Hom.:

14135

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.543

Gnomad AMR

AF:

0.571

Gnomad ASJ

AF:

0.315

Gnomad EAS

AF:

0.799

Gnomad SAS

AF:

0.472

Gnomad FIN

AF:

0.601

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.443

Gnomad OTH

AF:

0.384

GnomAD4 exome

AF:

0.453

AC:

651310

AN:

1436754

Hom.:

154415

Cov.:

AF XY:

0.452

AC XY:

323039

AN XY:

714826

show subpopulations

African (AFR)

AF:

0.0982

AC:

3238

AN:

32974

American (AMR)

AF:

0.694

AC:

30425

AN:

43840

Ashkenazi Jewish (ASJ)

AF:

0.315

AC:

8060

AN:

25612

East Asian (EAS)

AF:

0.810

AC:

31789

AN:

39260

South Asian (SAS)

AF:

0.453

AC:

38791

AN:

85610

European-Finnish (FIN)

AF:

0.578

AC:

29939

AN:

51802

Middle Eastern (MID)

AF:

0.344

AC:

1558

AN:

4526

European-Non Finnish (NFE)

AF:

0.441

AC:

481981

AN:

1094094

Other (OTH)

AF:

0.432

AC:

25529

AN:

59036

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.535

Heterozygous variant carriers

18871

37742

56613

75484

94355

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14616

29232

43848

58464

73080

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.387

AC:

58840

AN:

152058

Hom.:

14144

Cov.:

AF XY:

0.400

AC XY:

29770

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.115

AC:

4768

AN:

41514

American (AMR)

AF:

0.571

AC:

8738

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.315

AC:

1093

AN:

3470

East Asian (EAS)

AF:

0.798

AC:

4103

AN:

5142

South Asian (SAS)

AF:

0.471

AC:

2273

AN:

4822

European-Finnish (FIN)

AF:

0.601

AC:

6356

AN:

10576

Middle Eastern (MID)

AF:

0.289

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.443

AC:

30118

AN:

67934

Other (OTH)

AF:

0.386

AC:

814

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1643

3286

4928

6571

8214

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

554

1108

1662

2216

2770

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.395

Hom.:

11482

Bravo

AF:

0.380

Asia WGS

AF:

0.560

AC:

1944

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.85

(source)

DANN

Benign

0.77

PhyloP100

-0.037

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over