rs2071570

chr17-40100837-C-Achr17-40100837-C-G

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 0.237 in 189,340 control chromosomes in the GnomAD database, including 5,926 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 0.25 (4988 hom., cov: 33)
  • Exomes 𝑓: 0.20 (938 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37264 AN: 152074 Hom.: 4980 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.216

GnomAD4 exome AF: 0.205 AC: 7614 AN: 37148 Hom.: 938 AF XY: 0.206 AC XY: 3820 AN XY: 18574

Gnomad4 AFR exome AF: 0.208

Gnomad4 AMR exome AF: 0.131

Gnomad4 ASJ exome AF: 0.188

Gnomad4 EAS exome AF: 0.420

Gnomad4 SAS exome AF: 0.135

Gnomad4 FIN exome AF: 0.261

Gnomad4 NFE exome AF: 0.181

Gnomad4 OTH exome AF: 0.203

GnomAD4 genome AF: 0.245 AC: 37306 AN: 152192 Hom.: 4988 Cov.: 33 AF XY: 0.245 AC XY: 18226 AN XY: 74400

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.215

Alfa AF: 0.222 Hom.: 7903

Bravo AF: 0.238

Asia WGS AF: 0.341 AC: 1185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	3.1
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2071570; hg19: chr17-38257090; COSMIC: COSV55857863;