chr8-49628149-T-C

Variant names:

• chr8-49628149-T-C
• rs1496306

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 0.861 in 151,950 control chromosomes in the GnomAD database, including 56,710 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 0.86 (56710 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130677 AN: 151836 Hom.: 56671 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.859

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.861 AC: 130773 AN: 151950 Hom.: 56710 Cov.: 32 AF XY: 0.863 AC XY: 64076 AN XY: 74286

African (AFR) AF: 0.748 AC: 31013 AN: 41448

American (AMR) AF: 0.849 AC: 12947 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 3263 AN: 3470

East Asian (EAS) AF: 0.910 AC: 4692 AN: 5154

South Asian (SAS) AF: 0.813 AC: 3917 AN: 4818

European-Finnish (FIN) AF: 0.964 AC: 10194 AN: 10580

Middle Eastern (MID) AF: 0.869 AC: 252 AN: 290

European-Non Finnish (NFE) AF: 0.911 AC: 61883 AN: 67930

Other (OTH) AF: 0.851 AC: 1789 AN: 2102

Alfa AF: 0.895 Hom.: 25493

Bravo AF: 0.847

Asia WGS AF: 0.847 AC: 2915 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.56
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs1496306; hg19: chr8-50540708;