rs17391002

Variant names:

• chr10-44360479-A-G
• rs17391002

Your query was ambiguous. Multiple possible variants found:

• chr10-44360479-A-G
• chr10-44360479-A-T

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 0.24 in 152,094 control chromosomes in the GnomAD database, including 4,625 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 0.24 (4625 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 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: 0.240 AC: 36417 AN: 151976 Hom.: 4619 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.240 AC: 36459 AN: 152094 Hom.: 4625 Cov.: 32 AF XY: 0.238 AC XY: 17705 AN XY: 74370

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.230

Alfa AF: 0.223 Hom.: 3406

Bravo AF: 0.248

Asia WGS AF: 0.166 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17391002; hg19: chr10-44855927;