rs3775971

Variant names:

• chr4-103720763-T-C
• rs3775971

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 0.335 in 152,096 control chromosomes in the GnomAD database, including 13,214 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 0.34 (13214 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50885 AN: 151978 Hom.: 13171 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.335 AC: 50987 AN: 152096 Hom.: 13214 Cov.: 32 AF XY: 0.335 AC XY: 24885 AN XY: 74344

African (AFR) AF: 0.725 AC: 30068 AN: 41462

American (AMR) AF: 0.243 AC: 3723 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 595 AN: 3462

East Asian (EAS) AF: 0.358 AC: 1846 AN: 5154

South Asian (SAS) AF: 0.329 AC: 1581 AN: 4810

European-Finnish (FIN) AF: 0.175 AC: 1851 AN: 10580

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10436 AN: 68014

Other (OTH) AF: 0.306 AC: 646 AN: 2114

Alfa AF: 0.303 Hom.: 2584

Bravo AF: 0.355

Asia WGS AF: 0.366 AC: 1275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.69
DANN	Benign	0.34
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs3775971; hg19: chr4-104641920;