chr2-117174661-C-T

Variant names:

• chr2-117174661-C-T
• rs729253

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 0.49 in 151,998 control chromosomes in the GnomAD database, including 20,997 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 0.49 (20997 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 5 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 (EAS) allele frequency at 95% confidence interval = 0.769 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: 0.490 AC: 74437 AN: 151880 Hom.: 20986 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.490 AC: 74469 AN: 151998 Hom.: 20997 Cov.: 32 AF XY: 0.501 AC XY: 37226 AN XY: 74298

African (AFR) AF: 0.202 AC: 8395 AN: 41458

American (AMR) AF: 0.687 AC: 10473 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1939 AN: 3466

East Asian (EAS) AF: 0.789 AC: 4075 AN: 5162

South Asian (SAS) AF: 0.656 AC: 3164 AN: 4822

European-Finnish (FIN) AF: 0.609 AC: 6434 AN: 10558

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38217 AN: 67966

Other (OTH) AF: 0.531 AC: 1119 AN: 2108

Alfa AF: 0.539 Hom.: 10598

Bravo AF: 0.485

Asia WGS AF: 0.682 AC: 2368 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	1.9
DANN	Benign	0.63
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs729253; hg19: chr2-117932237;