rs17229970

Variant names:

• chr10-31681473-A-G
• rs17229970

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 0.168 in 152,070 control chromosomes in the GnomAD database, including 2,578 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 0.17 (2578 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.229 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: 0.168 AC: 25560 AN: 151952 Hom.: 2579 Cov.: 31

Gnomad AFR AF: 0.0613

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.168 AC: 25564 AN: 152070 Hom.: 2578 Cov.: 31 AF XY: 0.171 AC XY: 12687 AN XY: 74332

Gnomad4 AFR AF: 0.0612

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.172

Alfa AF: 0.194 Hom.: 408

Bravo AF: 0.163

Asia WGS AF: 0.119 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17229970; hg19: chr10-31970401;