Genetic Variant ENST00000522601.5:n.904+28T>A (chr8-8237303-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000522601.5(FAM86B3P):n.904+28T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000102 in 976,326 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)

Exomes 𝑓: 0.0000010 ( 0 hom. )

Consequence

FAM86B3P
ENST00000522601.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03

Publications

0 publications found

Variant links:

Genes affected

FAM86B3P (HGNC:):

FAM86B3P links:

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

FAM85B links:

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

ALG1L13P links:

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

FAM86B3P links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522601.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
FAM86B3P	NR_024361.1	n.929+28T>A	intron	N/A
FAM86B3P	NR_024362.1	n.1026+28T>A	intron	N/A
FAM86B3P	NR_024363.1	n.656+28T>A	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
FAM86B3P	ENST00000522601.5	TSL:1	n.904+28T>A	intron	N/A
FAM86B3P	ENST00000588728.5	TSL:1	n.626+28T>A	intron	N/A
FAM85B	ENST00000834326.1		n.891A>T	non_coding_transcript_exon	Exon 7 of 7

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000102

AC:

AN:

976326

Hom.:

Cov.:

AF XY:

0.00000198

AC XY:

AN XY:

505588

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

24394

American (AMR)

AF:

0.00

AC:

AN:

42890

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

22334

East Asian (EAS)

AF:

0.00

AC:

AN:

34210

South Asian (SAS)

AF:

0.00

AC:

AN:

77348

European-Finnish (FIN)

AF:

0.00

AC:

AN:

38872

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3230

European-Non Finnish (NFE)

AF:

0.00000145

AC:

AN:

689574

Other (OTH)

AF:

0.00

AC:

AN:

43474

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.91

(source)

DANN

Benign

0.53

PhyloP100

-1.0

Splicing

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

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over