rs924080

Variant names:

• chr1-67294457-T-C
• rs924080

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 0.446 in 152,026 control chromosomes in the GnomAD database, including 15,596 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 0.45 (15596 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 51 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.479 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: 0.446 AC: 67779 AN: 151908 Hom.: 15587 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.446 AC: 67823 AN: 152026 Hom.: 15596 Cov.: 32 AF XY: 0.438 AC XY: 32547 AN XY: 74320

African (AFR) AF: 0.484 AC: 20078 AN: 41464

American (AMR) AF: 0.439 AC: 6716 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1677 AN: 3468

East Asian (EAS) AF: 0.244 AC: 1263 AN: 5176

South Asian (SAS) AF: 0.315 AC: 1517 AN: 4822

European-Finnish (FIN) AF: 0.338 AC: 3567 AN: 10546

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31447 AN: 67950

Other (OTH) AF: 0.432 AC: 911 AN: 2110

Alfa AF: 0.456 Hom.: 54009

Bravo AF: 0.457

Asia WGS AF: 0.300 AC: 1048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.7
DANN	Benign	0.87
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs924080; hg19: chr1-67760140; COSMIC: COSV59951665;