6-153952815-A-G

Variant names:

• chr6-153952815-A-G
• rs493335

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 0.799 in 152,156 control chromosomes in the GnomAD database, including 48,955 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 0.80 (48955 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.441
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121512 AN: 152038 Hom.: 48929 Cov.: 32

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.799 AC: 121586 AN: 152156 Hom.: 48955 Cov.: 32 AF XY: 0.802 AC XY: 59642 AN XY: 74392

African (AFR) AF: 0.888 AC: 36867 AN: 41526

American (AMR) AF: 0.833 AC: 12708 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2330 AN: 3472

East Asian (EAS) AF: 0.756 AC: 3916 AN: 5180

South Asian (SAS) AF: 0.788 AC: 3805 AN: 4826

European-Finnish (FIN) AF: 0.823 AC: 8714 AN: 10594

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.745 AC: 50647 AN: 67982

Other (OTH) AF: 0.778 AC: 1641 AN: 2110

Alfa AF: 0.766 Hom.: 15034

Bravo AF: 0.804

Asia WGS AF: 0.757 AC: 2632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.79
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs493335; hg19: chr6-154273950;