chr1-17962758-T-C

Variant names:

• chr1-17962758-T-C
• rs794230

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 0.928 in 152,234 control chromosomes in the GnomAD database, including 65,909 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 0.93 (65909 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.987 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: 0.928 AC: 141127 AN: 152116 Hom.: 65878 Cov.: 32

Gnomad AFR AF: 0.847

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.990

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.993

Gnomad OTH AF: 0.933

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

GnomAD4 genome AF: 0.928 AC: 141212 AN: 152234 Hom.: 65909 Cov.: 32 AF XY: 0.925 AC XY: 68831 AN XY: 74418

African (AFR) AF: 0.847 AC: 35158 AN: 41514

American (AMR) AF: 0.847 AC: 12958 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.990 AC: 3436 AN: 3472

East Asian (EAS) AF: 0.812 AC: 4189 AN: 5162

South Asian (SAS) AF: 0.924 AC: 4446 AN: 4810

European-Finnish (FIN) AF: 0.967 AC: 10265 AN: 10618

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.993 AC: 67588 AN: 68036

Other (OTH) AF: 0.932 AC: 1973 AN: 2116

Alfa AF: 0.960 Hom.: 165599

Bravo AF: 0.913

Asia WGS AF: 0.878 AC: 3057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.0
DANN	Benign	0.79
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs794230; hg19: chr1-18289252;