rs10491098

Variant names:

• chr17-31801098-T-C
• rs10491098

Your query was ambiguous. Multiple possible variants found:

• chr17-31801098-T-C
• chr17-31801098-T-G

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 0.108 in 152,154 control chromosomes in the GnomAD database, including 1,902 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 0.11 (1902 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.397
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 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: 0.107 AC: 16309 AN: 152034 Hom.: 1891 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0636

Gnomad ASJ AF: 0.0619

Gnomad EAS AF: 0.0476

Gnomad SAS AF: 0.0752

Gnomad FIN AF: 0.0217

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0255

Gnomad OTH AF: 0.0994

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

GnomAD4 genome AF: 0.108 AC: 16359 AN: 152154 Hom.: 1902 Cov.: 32 AF XY: 0.105 AC XY: 7801 AN XY: 74376

African (AFR) AF: 0.298 AC: 12375 AN: 41488

American (AMR) AF: 0.0634 AC: 968 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0619 AC: 215 AN: 3472

East Asian (EAS) AF: 0.0477 AC: 247 AN: 5180

South Asian (SAS) AF: 0.0751 AC: 362 AN: 4820

European-Finnish (FIN) AF: 0.0217 AC: 230 AN: 10594

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0255 AC: 1734 AN: 68006

Other (OTH) AF: 0.0998 AC: 211 AN: 2114

Alfa AF: 0.0273 Hom.: 48

Bravo AF: 0.118

Asia WGS AF: 0.103 AC: 358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.42
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs10491098; hg19: chr17-30128117;