1-17962758-T-C

Position:

• chr1-17962758-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 0.928 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.17962758T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.847

Gnomad4 ASJ AF: 0.990

Gnomad4 EAS AF: 0.812

Gnomad4 SAS AF: 0.924

Gnomad4 FIN AF: 0.967

Gnomad4 NFE AF: 0.993

Gnomad4 OTH AF: 0.932

Alfa AF: 0.973 Hom.: 108710

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs794230; hg19: chr1-18289252;