rs626150

Variant names:

• chr6-153950003-T-C
• rs626150

Your query was ambiguous. Multiple possible variants found:

• chr6-153950003-T-C
• chr6-153950003-T-G

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 151,914 control chromosomes in the GnomAD database, including 48,840 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 (48840 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121283 AN: 151796 Hom.: 48814 Cov.: 32

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.671

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: 121357 AN: 151914 Hom.: 48840 Cov.: 32 AF XY: 0.801 AC XY: 59508 AN XY: 74250

African (AFR) AF: 0.888 AC: 36807 AN: 41464

American (AMR) AF: 0.833 AC: 12710 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2322 AN: 3464

East Asian (EAS) AF: 0.756 AC: 3893 AN: 5152

South Asian (SAS) AF: 0.788 AC: 3795 AN: 4816

European-Finnish (FIN) AF: 0.822 AC: 8663 AN: 10536

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.745 AC: 50562 AN: 67900

Other (OTH) AF: 0.779 AC: 1643 AN: 2110

Alfa AF: 0.771 Hom.: 5884

Bravo AF: 0.804

Asia WGS AF: 0.757 AC: 2632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.11
DANN	Benign	0.48
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs626150; hg19: chr6-154271138; COSMIC: COSV107167847;