rs714939

Variant names:

• chr2-75607981-G-A
• rs714939

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.409 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

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.404

Alfa AF: 0.408 Hom.: 1593

Bravo AF: 0.411

Asia WGS AF: 0.400 AC: 1396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs714939; hg19: chr2-75835107;