2-210737692-T-C

Variant names:

• chr2-210737692-T-C
• rs16844874

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.159 in 152,222 control chromosomes in the GnomAD database, including 2,286 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 0.16 (2286 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.196 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: 0.159 AC: 24148 AN: 152104 Hom.: 2282 Cov.: 32

Gnomad AFR AF: 0.0598

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.159 AC: 24153 AN: 152222 Hom.: 2286 Cov.: 32 AF XY: 0.166 AC XY: 12347 AN XY: 74430

Gnomad4 AFR AF: 0.0597

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.150

Alfa AF: 0.169 Hom.: 438

Bravo AF: 0.146

Asia WGS AF: 0.159 AC: 556 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	11
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16844874; hg19: chr2-211602416;