rs713586

chr2-24935139-T-C

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 0.569 in 152,050 control chromosomes in the GnomAD database, including 27,283 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 0.57 (27283 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86434 AN: 151932 Hom.: 27219 Cov.: 31

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.569 AC: 86544 AN: 152050 Hom.: 27283 Cov.: 31 AF XY: 0.559 AC XY: 41521 AN XY: 74322

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.527

Alfa AF: 0.481 Hom.: 15555

Bravo AF: 0.581

Asia WGS AF: 0.459 AC: 1596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.28
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs713586; hg19: chr2-25158008;