rs6656743

Variant names:

• chr1-154580974-T-A
• rs6656743

Your query was ambiguous. Multiple possible variants found:

• chr1-154580974-T-A
• chr1-154580974-T-C
• chr1-154580974-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 0.627 in 152,144 control chromosomes in the GnomAD database, including 31,004 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 0.63 (31004 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.746 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: 0.627 AC: 95346 AN: 152026 Hom.: 30991 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.627 AC: 95389 AN: 152144 Hom.: 31004 Cov.: 32 AF XY: 0.632 AC XY: 46982 AN XY: 74390

African (AFR) AF: 0.442 AC: 18309 AN: 41466

American (AMR) AF: 0.728 AC: 11132 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2538 AN: 3470

East Asian (EAS) AF: 0.705 AC: 3653 AN: 5182

South Asian (SAS) AF: 0.766 AC: 3699 AN: 4826

European-Finnish (FIN) AF: 0.651 AC: 6895 AN: 10594

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 47006 AN: 67994

Other (OTH) AF: 0.639 AC: 1349 AN: 2110

Alfa AF: 0.565 Hom.: 1795

Bravo AF: 0.624

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.2
DANN	Benign	0.59
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs6656743; hg19: chr1-154553450;