2-49809545-G-T

Variant names:

• chr2-49809545-G-T
• rs11690252

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 0.316 in 151,890 control chromosomes in the GnomAD database, including 8,021 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 0.32 (8021 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.418 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: 0.315 AC: 47883 AN: 151772 Hom.: 8013 Cov.: 31

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.316 AC: 47924 AN: 151890 Hom.: 8021 Cov.: 31 AF XY: 0.311 AC XY: 23114 AN XY: 74238

African (AFR) AF: 0.423 AC: 17540 AN: 41420

American (AMR) AF: 0.230 AC: 3512 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1126 AN: 3470

East Asian (EAS) AF: 0.250 AC: 1285 AN: 5150

South Asian (SAS) AF: 0.385 AC: 1854 AN: 4812

European-Finnish (FIN) AF: 0.219 AC: 2315 AN: 10554

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19316 AN: 67922

Other (OTH) AF: 0.308 AC: 648 AN: 2102

Alfa AF: 0.177 Hom.: 409

Bravo AF: 0.316

Asia WGS AF: 0.329 AC: 1145 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.53
DANN	Benign	0.29
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs11690252; hg19: chr2-50036683;