4-161291560-C-T

Variant names:

• chr4-161291560-C-T
• rs1961435

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 0.21 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.210 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

Gnomad4 AFR AF: 0.0645

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.243

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1961435; hg19: chr4-162212712;