rs13074924

Positions:

• chr3-174311255-A-G
• chr3-174311255-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.647 in 151,914 control chromosomes in the GnomAD database, including 32,058 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 0.65 (32058 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98157 AN: 151796 Hom.: 32040 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.647 AC: 98231 AN: 151914 Hom.: 32058 Cov.: 32 AF XY: 0.649 AC XY: 48237 AN XY: 74272

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.831

Gnomad4 SAS AF: 0.619

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.666

Alfa AF: 0.650 Hom.: 48615

Bravo AF: 0.647

Asia WGS AF: 0.728 AC: 2528 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13074924; hg19: chr3-174029045;