rs612692

Variant names:

• chr6-153950642-T-A
• rs612692

Your query was ambiguous. Multiple possible variants found:

• chr6-153950642-T-A
• chr6-153950642-T-C
• chr6-153950642-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 152,078 control chromosomes in the GnomAD database, including 48,929 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 (48929 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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: 121464 AN: 151960 Hom.: 48903 Cov.: 32

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.824

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: 121538 AN: 152078 Hom.: 48929 Cov.: 32 AF XY: 0.802 AC XY: 59616 AN XY: 74340

African (AFR) AF: 0.888 AC: 36858 AN: 41514

American (AMR) AF: 0.832 AC: 12713 AN: 15272

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

East Asian (EAS) AF: 0.756 AC: 3907 AN: 5168

South Asian (SAS) AF: 0.788 AC: 3801 AN: 4822

European-Finnish (FIN) AF: 0.824 AC: 8696 AN: 10558

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

European-Non Finnish (NFE) AF: 0.745 AC: 50635 AN: 67964

Other (OTH) AF: 0.778 AC: 1636 AN: 2102

Alfa AF: 0.684 Hom.: 1956

Bravo AF: 0.804

Asia WGS AF: 0.756 AC: 2629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.57
DANN	Benign	0.23
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs612692; hg19: chr6-154271777; COSMIC: COSV107167848;