chr2-127139435-T-C

Variant names:

• chr2-127139435-T-C
• rs6759460

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 0.267 in 152,110 control chromosomes in the GnomAD database, including 5,704 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 0.27 (5704 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.434 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: 0.267 AC: 40610 AN: 151992 Hom.: 5694 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.267 AC: 40656 AN: 152110 Hom.: 5704 Cov.: 32 AF XY: 0.269 AC XY: 19980 AN XY: 74372

African (AFR) AF: 0.283 AC: 11749 AN: 41470

American (AMR) AF: 0.268 AC: 4095 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1376 AN: 3466

East Asian (EAS) AF: 0.449 AC: 2318 AN: 5164

South Asian (SAS) AF: 0.314 AC: 1514 AN: 4820

European-Finnish (FIN) AF: 0.242 AC: 2568 AN: 10592

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.238 AC: 16164 AN: 67994

Other (OTH) AF: 0.288 AC: 608 AN: 2114

Alfa AF: 0.243 Hom.: 587

Bravo AF: 0.273

Asia WGS AF: 0.351 AC: 1222 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.64
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs6759460; hg19: chr2-127897011;