2-210779923-T-G

Variant names:

• chr2-210779923-T-G
• rs10172053

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 0.173 in 151,998 control chromosomes in the GnomAD database, including 2,448 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 0.17 (2448 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.199 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: 0.173 AC: 26264 AN: 151880 Hom.: 2444 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.173 AC: 26276 AN: 151998 Hom.: 2448 Cov.: 32 AF XY: 0.179 AC XY: 13268 AN XY: 74312

African (AFR) AF: 0.117 AC: 4844 AN: 41440

American (AMR) AF: 0.205 AC: 3124 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 569 AN: 3462

East Asian (EAS) AF: 0.153 AC: 790 AN: 5168

South Asian (SAS) AF: 0.195 AC: 941 AN: 4818

European-Finnish (FIN) AF: 0.295 AC: 3116 AN: 10574

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12355 AN: 67966

Other (OTH) AF: 0.155 AC: 327 AN: 2110

Alfa AF: 0.164 Hom.: 2706

Bravo AF: 0.164

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.46
DANN	Benign	0.68
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs10172053; hg19: chr2-211644647;