rs3756261

chr4-109911150-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;