rs17312292

Positions:

• chr1-175746470-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 49 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.00168

Gnomad4 AMR AF: 0.00333

Gnomad4 ASJ AF: 0.00663

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0232

Gnomad4 FIN AF: 0.0839

Gnomad4 NFE AF: 0.0137

Gnomad4 OTH AF: 0.00994

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17312292; hg19: chr1-175715606;