chr2-75607981-G-A

Variant names:

• chr2-75607981-G-A
• rs714939

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 0.409 in 151,976 control chromosomes in the GnomAD database, including 12,747 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 0.41 (12747 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.509
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62085 AN: 151858 Hom.: 12734 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.409 AC: 62130 AN: 151976 Hom.: 12747 Cov.: 32 AF XY: 0.410 AC XY: 30450 AN XY: 74296

African (AFR) AF: 0.428 AC: 17707 AN: 41418

American (AMR) AF: 0.419 AC: 6402 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1541 AN: 3470

East Asian (EAS) AF: 0.361 AC: 1858 AN: 5152

South Asian (SAS) AF: 0.418 AC: 2013 AN: 4812

European-Finnish (FIN) AF: 0.452 AC: 4773 AN: 10564

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26380 AN: 67968

Other (OTH) AF: 0.404 AC: 854 AN: 2116

Alfa AF: 0.408 Hom.: 1663

Bravo AF: 0.411

Asia WGS AF: 0.400 AC: 1396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.7
DANN	Benign	0.71
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs714939; hg19: chr2-75835107;