rs17391694

Variant names:

• chr1-78157942-C-T
• rs17391694

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 0.0767 in 152,212 control chromosomes in the GnomAD database, including 690 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 0.077 (690 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 94 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 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: 0.0768 AC: 11681 AN: 152094 Hom.: 690 Cov.: 32

Gnomad AFR AF: 0.0212

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0554

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0118

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0608

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

GnomAD4 genome AF: 0.0767 AC: 11680 AN: 152212 Hom.: 690 Cov.: 32 AF XY: 0.0749 AC XY: 5577 AN XY: 74428

African (AFR) AF: 0.0211 AC: 878 AN: 41550

American (AMR) AF: 0.0553 AC: 846 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0271 AC: 94 AN: 3470

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5190

South Asian (SAS) AF: 0.0118 AC: 57 AN: 4822

European-Finnish (FIN) AF: 0.122 AC: 1290 AN: 10586

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8291 AN: 67984

Other (OTH) AF: 0.0602 AC: 127 AN: 2110

Alfa AF: 0.102 Hom.: 3709

Bravo AF: 0.0710

Asia WGS AF: 0.00779 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.21
DANN	Benign	0.67
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs17391694; hg19: chr1-78623626;