1-43109931-C-T

Variant names:

• chr1-43109931-C-T
• rs498166

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 0.289 in 152,110 control chromosomes in the GnomAD database, including 10,119 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 0.29 (10119 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 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: 0.289 AC: 43903 AN: 151992 Hom.: 10079 Cov.: 33

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.0975

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.289 AC: 43997 AN: 152110 Hom.: 10119 Cov.: 33 AF XY: 0.297 AC XY: 22057 AN XY: 74354

African (AFR) AF: 0.603 AC: 25003 AN: 41468

American (AMR) AF: 0.329 AC: 5025 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0975 AC: 338 AN: 3468

East Asian (EAS) AF: 0.545 AC: 2815 AN: 5164

South Asian (SAS) AF: 0.272 AC: 1311 AN: 4828

European-Finnish (FIN) AF: 0.190 AC: 2009 AN: 10592

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6885 AN: 68012

Other (OTH) AF: 0.240 AC: 505 AN: 2108

Alfa AF: 0.203 Hom.: 736

Bravo AF: 0.316

Asia WGS AF: 0.417 AC: 1446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.7
DANN	Benign	0.54
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs498166; hg19: chr1-43575602;