chr1-118342291-A-C

Variant names:

• chr1-118342291-A-C
• rs2474945

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 0.195 in 152,174 control chromosomes in the GnomAD database, including 3,032 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 0.19 (3032 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 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: 0.195 AC: 29590 AN: 152056 Hom.: 3030 Cov.: 33

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.0754

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.195 AC: 29618 AN: 152174 Hom.: 3032 Cov.: 33 AF XY: 0.193 AC XY: 14335 AN XY: 74390

African (AFR) AF: 0.154 AC: 6406 AN: 41514

American (AMR) AF: 0.200 AC: 3056 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 629 AN: 3468

East Asian (EAS) AF: 0.0752 AC: 389 AN: 5174

South Asian (SAS) AF: 0.265 AC: 1278 AN: 4816

European-Finnish (FIN) AF: 0.188 AC: 1989 AN: 10580

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15024 AN: 68006

Other (OTH) AF: 0.216 AC: 457 AN: 2112

Alfa AF: 0.208 Hom.: 826

Bravo AF: 0.193

Asia WGS AF: 0.167 AC: 587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.94
DANN	Benign	0.70
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs2474945; hg19: chr1-118884914;