rs10498093

Variant names:

• chr2-220915923-C-T
• rs10498093

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.00794 in 152,124 control chromosomes in the GnomAD database, including 21 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 0.0079 (21 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.00794 (1208/152124) while in subpopulation SAS AF = 0.0515 (248/4818). AF 95% confidence interval is 0.0462. There are 21 homozygotes in GnomAd4. There are 638 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position FAILED quality control check.
• BS2: High Homozygotes in GnomAd4 at 21 gene

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: 0.00794 AC: 1207 AN: 152006 Hom.: 21 Cov.: 32

Gnomad AFR AF: 0.00152

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00498

Gnomad ASJ AF: 0.00894

Gnomad EAS AF: 0.0381

Gnomad SAS AF: 0.0514

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.00804

Gnomad OTH AF: 0.00669

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

GnomAD4 genome AF: 0.00794 AC: 1208 AN: 152124 Hom.: 21 Cov.: 32 AF XY: 0.00858 AC XY: 638 AN XY: 74362

African (AFR) AF: 0.00154 AC: 64 AN: 41486

American (AMR) AF: 0.00497 AC: 76 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00894 AC: 31 AN: 3466

East Asian (EAS) AF: 0.0380 AC: 196 AN: 5160

South Asian (SAS) AF: 0.0515 AC: 248 AN: 4818

European-Finnish (FIN) AF: 0.00113 AC: 12 AN: 10588

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.00803 AC: 546 AN: 68002

Other (OTH) AF: 0.00851 AC: 18 AN: 2114

Alfa AF: 0.00651 Hom.: 0

Bravo AF: 0.00739

Asia WGS AF: 0.0470 AC: 163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498093; hg19: chr2-221780643;