rs17646946

Variant names:

• chr1-152090291-G-A
• rs17646946

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 0.172 in 152,200 control chromosomes in the GnomAD database, including 2,606 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 0.17 (2606 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 35 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.207 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: 0.172 AC: 26106 AN: 152082 Hom.: 2604 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.00424

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.172 AC: 26112 AN: 152200 Hom.: 2606 Cov.: 32 AF XY: 0.173 AC XY: 12864 AN XY: 74408

African (AFR) AF: 0.120 AC: 4988 AN: 41540

American (AMR) AF: 0.140 AC: 2142 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 459 AN: 3472

East Asian (EAS) AF: 0.00425 AC: 22 AN: 5180

South Asian (SAS) AF: 0.120 AC: 579 AN: 4832

European-Finnish (FIN) AF: 0.296 AC: 3133 AN: 10588

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

European-Non Finnish (NFE) AF: 0.210 AC: 14287 AN: 67980

Other (OTH) AF: 0.175 AC: 371 AN: 2116

Alfa AF: 0.188 Hom.: 13625

Bravo AF: 0.155

Asia WGS AF: 0.0710 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.0
DANN	Benign	0.68
PhyloP100		0.028

Splicing

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

Other links and lift over

dbSNP: rs17646946; hg19: chr1-152062767;