rs2249596

Variant names:

• chr5-135012266-T-C
• rs2249596

Your query was ambiguous. Multiple possible variants found:

• chr5-135012266-T-C
• chr5-135012266-T-G

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 0.354 in 152,058 control chromosomes in the GnomAD database, including 9,886 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 0.35 (9886 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.503 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: 0.354 AC: 53749 AN: 151938 Hom.: 9873 Cov.: 33

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.354 AC: 53794 AN: 152058 Hom.: 9886 Cov.: 33 AF XY: 0.357 AC XY: 26555 AN XY: 74322

African (AFR) AF: 0.405 AC: 16803 AN: 41486

American (AMR) AF: 0.368 AC: 5626 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 983 AN: 3466

East Asian (EAS) AF: 0.503 AC: 2593 AN: 5156

South Asian (SAS) AF: 0.519 AC: 2506 AN: 4824

European-Finnish (FIN) AF: 0.302 AC: 3191 AN: 10580

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20878 AN: 67942

Other (OTH) AF: 0.338 AC: 712 AN: 2108

Alfa AF: 0.313 Hom.: 6285

Bravo AF: 0.357

Asia WGS AF: 0.550 AC: 1911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
DANN	Benign	0.62
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs2249596; hg19: chr5-134347956; COSMIC: COSV50945607;