2-5136102-T-G

Variant names:

• chr2-5136102-T-G
• rs17265240

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 0.172 in 152,220 control chromosomes in the GnomAD database, including 2,819 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 (2819 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.238 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: 0.172 AC: 26142 AN: 152102 Hom.: 2821 Cov.: 32

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.0764

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.172 AC: 26136 AN: 152220 Hom.: 2819 Cov.: 32 AF XY: 0.172 AC XY: 12772 AN XY: 74408

African (AFR) AF: 0.0411 AC: 1707 AN: 41574

American (AMR) AF: 0.155 AC: 2371 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 964 AN: 3468

East Asian (EAS) AF: 0.0762 AC: 394 AN: 5170

South Asian (SAS) AF: 0.204 AC: 986 AN: 4822

European-Finnish (FIN) AF: 0.248 AC: 2621 AN: 10578

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16374 AN: 67988

Other (OTH) AF: 0.186 AC: 392 AN: 2112

Alfa AF: 0.186 Hom.: 2018

Bravo AF: 0.159

Asia WGS AF: 0.146 AC: 509 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.8
DANN	Benign	0.66
PhyloP100		-0.038

Splicing

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

Other links and lift over

dbSNP: rs17265240; hg19: chr2-5276235;