rs10498122

Positions:

• chr2-221811794-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0307 in 152,234 control chromosomes in the GnomAD database, including 107 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 0.031 (107 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0307 (4674/152234) while in subpopulation NFE AF= 0.0485 (3298/68010). AF 95% confidence interval is 0.0471. There are 107 homozygotes in gnomad4. There are 2246 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 107 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0307 AC: 4676 AN: 152116 Hom.: 107 Cov.: 32

Gnomad AFR AF: 0.00792

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.0204

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.0404

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0485

Gnomad OTH AF: 0.0291

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

GnomAD4 genome AF: 0.0307 AC: 4674 AN: 152234 Hom.: 107 Cov.: 32 AF XY: 0.0302 AC XY: 2246 AN XY: 74446

Gnomad4 AFR AF: 0.00789

Gnomad4 AMR AF: 0.0203

Gnomad4 ASJ AF: 0.0213

Gnomad4 EAS AF: 0.000581

Gnomad4 SAS AF: 0.0346

Gnomad4 FIN AF: 0.0404

Gnomad4 NFE AF: 0.0485

Gnomad4 OTH AF: 0.0284

Alfa AF: 0.0441 Hom.: 29

Bravo AF: 0.0262

Asia WGS AF: 0.0100 AC: 37 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498122; hg19: chr2-222676514;