rs3912601

Positions:

• chr3-73362536-C-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 0.33 in 152,038 control chromosomes in the GnomAD database, including 8,601 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 0.33 (8601 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.984

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 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: 0.330 AC: 50191 AN: 151920 Hom.: 8589 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.330 AC: 50223 AN: 152038 Hom.: 8601 Cov.: 32 AF XY: 0.335 AC XY: 24879 AN XY: 74314

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.366

Alfa AF: 0.306 Hom.: 15023

Bravo AF: 0.337

Asia WGS AF: 0.481 AC: 1674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3912601; hg19: chr3-73411687;