rs17312292

Variant names:

• chr1-175746470-G-C
• rs17312292

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0148 in 152,302 control chromosomes in the GnomAD database, including 49 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 0.015 (49 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.724
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0148 (2254/152302) while in subpopulation SAS AF = 0.0232 (112/4822). AF 95% confidence interval is 0.0197. There are 49 homozygotes in GnomAd4. There are 1307 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 49 gene

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: 0.0148 AC: 2254 AN: 152184 Hom.: 49 Cov.: 32

Gnomad AFR AF: 0.00169

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.00334

Gnomad ASJ AF: 0.00663

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0234

Gnomad FIN AF: 0.0839

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0137

Gnomad OTH AF: 0.0100

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

GnomAD4 genome AF: 0.0148 AC: 2254 AN: 152302 Hom.: 49 Cov.: 32 AF XY: 0.0176 AC XY: 1307 AN XY: 74470

African (AFR) AF: 0.00168 AC: 70 AN: 41582

American (AMR) AF: 0.00333 AC: 51 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00663 AC: 23 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.0232 AC: 112 AN: 4822

European-Finnish (FIN) AF: 0.0839 AC: 891 AN: 10618

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

European-Non Finnish (NFE) AF: 0.0137 AC: 934 AN: 68012

Other (OTH) AF: 0.00994 AC: 21 AN: 2112

Alfa AF: 0.0136 Hom.: 3

Bravo AF: 0.00859

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	8.0
DANN	Benign	0.67
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs17312292; hg19: chr1-175715606;