chr1-115191470-T-C

Variant names:

• chr1-115191470-T-C
• rs195204

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 0.222 in 152,076 control chromosomes in the GnomAD database, including 4,342 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 0.22 (4342 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.689
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.435 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: 0.222 AC: 33779 AN: 151958 Hom.: 4337 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.222 AC: 33807 AN: 152076 Hom.: 4342 Cov.: 32 AF XY: 0.231 AC XY: 17139 AN XY: 74354

African (AFR) AF: 0.113 AC: 4691 AN: 41492

American (AMR) AF: 0.313 AC: 4781 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 932 AN: 3472

East Asian (EAS) AF: 0.392 AC: 2016 AN: 5148

South Asian (SAS) AF: 0.451 AC: 2172 AN: 4820

European-Finnish (FIN) AF: 0.232 AC: 2452 AN: 10580

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15897 AN: 67984

Other (OTH) AF: 0.234 AC: 495 AN: 2112

Alfa AF: 0.243 Hom.: 17199

Bravo AF: 0.224

Asia WGS AF: 0.396 AC: 1378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	7.2
DANN	Benign	0.69
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs195204; hg19: chr1-115734091; COSMIC: COSV59990488;