rs713586

Variant names:

• chr2-24935139-T-C
• rs713586
• ENST00000841804.1:n.189+10936T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000841804.1(ENSG00000309511):​n.189+10936T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000309511 ENST00000841804.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 173 publications found

Genes affected

ENSG00000309511 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000841804.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309511	ENST00000841804.1		n.189+10936T>C		intron	N/A

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

African (AFR) AF: 0.856 AC: 35531 AN: 41508

American (AMR) AF: 0.419 AC: 6393 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1482 AN: 3470

East Asian (EAS) AF: 0.477 AC: 2456 AN: 5152

South Asian (SAS) AF: 0.482 AC: 2323 AN: 4822

European-Finnish (FIN) AF: 0.403 AC: 4258 AN: 10560

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32511 AN: 67954

Other (OTH) AF: 0.527 AC: 1110 AN: 2106

Alfa AF: 0.502 Hom.: 55253

Bravo AF: 0.581

Asia WGS AF: 0.459 AC: 1596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.28
DANN	Benign	0.35
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs713586; hg19: chr2-25158008;