rs1634514

Positions:

• chr17-36103525-T-A
• chr17-36103525-T-C

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 0.196 in 329,076 control chromosomes in the GnomAD database, including 7,143 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 0.18 (2834 hom., cov: 30)
  • Exomes 𝑓: 0.21 (4309 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

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: 0.179 AC: 27071 AN: 151598 Hom.: 2833 Cov.: 30

Gnomad AFR AF: 0.0717

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.184

GnomAD4 exome AF: 0.210 AC: 37268 AN: 177360 Hom.: 4309 AF XY: 0.209 AC XY: 20001 AN XY: 95494

Gnomad4 AFR exome AF: 0.0667

Gnomad4 AMR exome AF: 0.191

Gnomad4 ASJ exome AF: 0.171

Gnomad4 EAS exome AF: 0.285

Gnomad4 SAS exome AF: 0.204

Gnomad4 FIN exome AF: 0.160

Gnomad4 NFE exome AF: 0.222

Gnomad4 OTH exome AF: 0.197

GnomAD4 genome AF: 0.178 AC: 27077 AN: 151716 Hom.: 2834 Cov.: 30 AF XY: 0.176 AC XY: 13065 AN XY: 74098

Gnomad4 AFR AF: 0.0719

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.182

Alfa AF: 0.199 Hom.: 415

Bravo AF: 0.179

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1634514; hg19: chr17-34430918;