1-161312594-T-C

Variant names:

• chr1-161312594-T-C
• rs4131826

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 0.262 in 152,114 control chromosomes in the GnomAD database, including 6,385 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 0.26 (6385 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.352 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: 0.262 AC: 39787 AN: 151996 Hom.: 6381 Cov.: 32

Gnomad AFR AF: 0.0741

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.262 AC: 39789 AN: 152114 Hom.: 6385 Cov.: 32 AF XY: 0.258 AC XY: 19203 AN XY: 74348

African (AFR) AF: 0.0739 AC: 3067 AN: 41514

American (AMR) AF: 0.286 AC: 4369 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1243 AN: 3466

East Asian (EAS) AF: 0.262 AC: 1358 AN: 5174

South Asian (SAS) AF: 0.289 AC: 1393 AN: 4820

European-Finnish (FIN) AF: 0.303 AC: 3194 AN: 10554

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24161 AN: 67986

Other (OTH) AF: 0.273 AC: 575 AN: 2108

Alfa AF: 0.297 Hom.: 9297

Bravo AF: 0.258

Asia WGS AF: 0.215 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.71
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs4131826; hg19: chr1-161282384;