8-103106338-A-G

Variant names:

• chr8-103106338-A-G
• rs6983777

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.508 in 152,040 control chromosomes in the GnomAD database, including 19,898 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 0.51 (19898 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.560
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77237 AN: 151922 Hom.: 19883 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.508 AC: 77288 AN: 152040 Hom.: 19898 Cov.: 32 AF XY: 0.507 AC XY: 37660 AN XY: 74318

African (AFR) AF: 0.553 AC: 22922 AN: 41428

American (AMR) AF: 0.537 AC: 8206 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1436 AN: 3466

East Asian (EAS) AF: 0.359 AC: 1862 AN: 5182

South Asian (SAS) AF: 0.527 AC: 2537 AN: 4814

European-Finnish (FIN) AF: 0.452 AC: 4772 AN: 10568

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33698 AN: 67982

Other (OTH) AF: 0.510 AC: 1078 AN: 2112

Alfa AF: 0.506 Hom.: 23690

Bravo AF: 0.517

Asia WGS AF: 0.418 AC: 1453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.0
DANN	Benign	0.78
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs6983777; hg19: chr8-104118566;