rs924674

Variant names:

• chr5-3741161-A-T
• rs924674

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 0.376 in 152,170 control chromosomes in the GnomAD database, including 11,855 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 0.38 (11855 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 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: 0.376 AC: 57215 AN: 152052 Hom.: 11848 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.376 AC: 57240 AN: 152170 Hom.: 11855 Cov.: 33 AF XY: 0.380 AC XY: 28242 AN XY: 74388

African (AFR) AF: 0.185 AC: 7673 AN: 41544

American (AMR) AF: 0.441 AC: 6742 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1364 AN: 3470

East Asian (EAS) AF: 0.459 AC: 2371 AN: 5170

South Asian (SAS) AF: 0.420 AC: 2024 AN: 4824

European-Finnish (FIN) AF: 0.471 AC: 4982 AN: 10576

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30806 AN: 67976

Other (OTH) AF: 0.392 AC: 826 AN: 2108

Alfa AF: 0.405 Hom.: 1636

Bravo AF: 0.366

Asia WGS AF: 0.430 AC: 1493 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	13
DANN	Benign	0.83
PhyloP100		-0.082

Splicing

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

Other links and lift over

dbSNP: rs924674; hg19: chr5-3741275;