rs10498093

Positions:

• chr2-220915923-C-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 0.00794 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 21 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.220915923C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.00154

Gnomad4 AMR AF: 0.00497

Gnomad4 ASJ AF: 0.00894

Gnomad4 EAS AF: 0.0380

Gnomad4 SAS AF: 0.0515

Gnomad4 FIN AF: 0.00113

Gnomad4 NFE AF: 0.00803

Gnomad4 OTH AF: 0.00851

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;