rs3756261

Variant names:

• chr4-109911150-T-C
• rs3756261

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 0.0991 in 152,142 control chromosomes in the GnomAD database, including 1,087 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 0.099 (1087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 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: 0.0989 AC: 15039 AN: 152024 Hom.: 1082 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.0941

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.0834

Gnomad FIN AF: 0.0427

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0514

Gnomad OTH AF: 0.0908

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

GnomAD4 genome AF: 0.0991 AC: 15076 AN: 152142 Hom.: 1087 Cov.: 32 AF XY: 0.101 AC XY: 7482 AN XY: 74402

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.0938

Gnomad4 ASJ AF: 0.0839

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.0841

Gnomad4 FIN AF: 0.0427

Gnomad4 NFE AF: 0.0515

Gnomad4 OTH AF: 0.0937

Alfa AF: 0.0779 Hom.: 183

Bravo AF: 0.107

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3756261; hg19: chr4-110832306;