1-161312594-T-C

Position:

• chr1-161312594-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 0.262 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0739

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.273

Alfa AF: 0.325 Hom.: 5413

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4131826; hg19: chr1-161282384;