rs17302632

Variant names:

• chr1-181070392-C-T
• rs17302632

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 0.0426 in 152,326 control chromosomes in the GnomAD database, including 172 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 0.043 (172 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0562 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: 0.0426 AC: 6480 AN: 152208 Hom.: 171 Cov.: 32

Gnomad AFR AF: 0.0278

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0394

Gnomad ASJ AF: 0.0816

Gnomad EAS AF: 0.0620

Gnomad SAS AF: 0.0521

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0479

Gnomad OTH AF: 0.0521

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

GnomAD4 genome AF: 0.0426 AC: 6482 AN: 152326 Hom.: 172 Cov.: 32 AF XY: 0.0413 AC XY: 3079 AN XY: 74498

Gnomad4 AFR AF: 0.0278

Gnomad4 AMR AF: 0.0395

Gnomad4 ASJ AF: 0.0816

Gnomad4 EAS AF: 0.0618

Gnomad4 SAS AF: 0.0526

Gnomad4 FIN AF: 0.0437

Gnomad4 NFE AF: 0.0479

Gnomad4 OTH AF: 0.0520

Alfa AF: 0.0485 Hom.: 217

Bravo AF: 0.0426

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.9
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17302632; hg19: chr1-181039528;