chr4-161291560-C-T

Variant names:

• chr4-161291560-C-T
• rs1961435

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 0.21 in 152,062 control chromosomes in the GnomAD database, including 4,089 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 0.21 (4089 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31918 AN: 151942 Hom.: 4089 Cov.: 32

Gnomad AFR AF: 0.0648

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.210 AC: 31917 AN: 152062 Hom.: 4089 Cov.: 32 AF XY: 0.209 AC XY: 15527 AN XY: 74314

African (AFR) AF: 0.0645 AC: 2677 AN: 41488

American (AMR) AF: 0.274 AC: 4179 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1079 AN: 3468

East Asian (EAS) AF: 0.268 AC: 1384 AN: 5164

South Asian (SAS) AF: 0.215 AC: 1037 AN: 4816

European-Finnish (FIN) AF: 0.234 AC: 2467 AN: 10562

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18317 AN: 67974

Other (OTH) AF: 0.243 AC: 513 AN: 2114

Alfa AF: 0.118 Hom.: 211

Bravo AF: 0.212

Asia WGS AF: 0.244 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.84
DANN	Benign	0.71
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs1961435; hg19: chr4-162212712;