rs1417096

Variant names:

• chr10-16105480-A-G
• rs1417096

Your query was ambiguous. Multiple possible variants found:

• chr10-16105480-A-G
• chr10-16105480-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 0.603 in 151,902 control chromosomes in the GnomAD database, including 28,532 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 0.60 (28532 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.681 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: 0.603 AC: 91562 AN: 151784 Hom.: 28526 Cov.: 31

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.603 AC: 91600 AN: 151902 Hom.: 28532 Cov.: 31 AF XY: 0.597 AC XY: 44342 AN XY: 74230

African (AFR) AF: 0.486 AC: 20121 AN: 41392

American (AMR) AF: 0.675 AC: 10311 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2356 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1526 AN: 5164

South Asian (SAS) AF: 0.442 AC: 2129 AN: 4812

European-Finnish (FIN) AF: 0.606 AC: 6397 AN: 10548

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.686 AC: 46617 AN: 67938

Other (OTH) AF: 0.627 AC: 1321 AN: 2106

Alfa AF: 0.647 Hom.: 13873

Bravo AF: 0.610

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.68
DANN	Benign	0.32
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1417096; hg19: chr10-16147479;