2-127137039-A-G

Variant names:

• chr2-127137039-A-G
• rs744373

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 0.348 in 151,870 control chromosomes in the GnomAD database, including 9,937 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 (9937 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 218 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.483 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: 0.347 AC: 52679 AN: 151752 Hom.: 9885 Cov.: 31

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.348 AC: 52802 AN: 151870 Hom.: 9937 Cov.: 31 AF XY: 0.343 AC XY: 25418 AN XY: 74206

African (AFR) AF: 0.489 AC: 20232 AN: 41402

American (AMR) AF: 0.371 AC: 5664 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1038 AN: 3470

East Asian (EAS) AF: 0.346 AC: 1779 AN: 5140

South Asian (SAS) AF: 0.217 AC: 1043 AN: 4816

European-Finnish (FIN) AF: 0.238 AC: 2510 AN: 10564

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.287 AC: 19489 AN: 67888

Other (OTH) AF: 0.333 AC: 704 AN: 2112

Alfa AF: 0.308 Hom.: 35458

Bravo AF: 0.367

Asia WGS AF: 0.349 AC: 1215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.9
DANN	Benign	0.82
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs744373; hg19: chr2-127894615;