dbSNP rs16887478: LOC105379384:n.8908G>A (chr8-38584525-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_007060891.1(LOC105379384):n.8908G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,106 control chromosomes in the GnomAD database, including 1,477 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 0.14 ( 1477 hom., cov: 33)

Consequence

LOC105379384
XR_007060891.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0410

Publications

3 publications found

Variant links:

Genes affected

LOC105379384 (HGNC:):

LOC105379384 links:

Genome browser will be placed here

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=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379384	XR_007060891.1 link	n.8908G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.135

AC:

20549

AN:

151988

Hom.:

1475

Cov.:

show subpopulations

Gnomad AFR

AF:

0.133

Gnomad AMI

AF:

0.198

Gnomad AMR

AF:

0.141

Gnomad ASJ

AF:

0.221

Gnomad EAS

AF:

0.0882

Gnomad SAS

AF:

0.117

Gnomad FIN

AF:

0.106

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.139

Gnomad OTH

AF:

0.136

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.135

AC:

20565

AN:

152106

Hom.:

1477

Cov.:

AF XY:

0.133

AC XY:

9901

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.133

AC:

5509

AN:

41498

American (AMR)

AF:

0.141

AC:

2150

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.221

AC:

766

AN:

3468

East Asian (EAS)

AF:

0.0886

AC:

459

AN:

5178

South Asian (SAS)

AF:

0.117

AC:

566

AN:

4820

European-Finnish (FIN)

AF:

0.106

AC:

1120

AN:

10568

Middle Eastern (MID)

AF:

0.180

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.139

AC:

9476

AN:

67974

Other (OTH)

AF:

0.135

AC:

285

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

910

1821

2731

3642

4552

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

236

472

708

944

1180

<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:

0.134

Hom.:

522

Bravo

AF:

0.139

Asia WGS

AF:

0.0890

AC:

310

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.0

(source)

DANN

Benign

0.28

PhyloP100

0.041

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over