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. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.322 AC: 13336 AN: 41450

American (AMR) AF: 0.238 AC: 3641 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 562 AN: 3470

East Asian (EAS) AF: 0.152 AC: 789 AN: 5174

South Asian (SAS) AF: 0.179 AC: 860 AN: 4810

European-Finnish (FIN) AF: 0.215 AC: 2280 AN: 10602

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14241 AN: 67998

Other (OTH) AF: 0.230 AC: 486 AN: 2110

Alfa AF: 0.225 Hom.: 5010

Bravo AF: 0.248

Asia WGS AF: 0.166 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.48
PhyloP100		-0.15
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs17391002; hg19: chr10-44855927;