2-24935412-C-T

Variant names:

• chr2-24935412-C-T
• rs713587
• ENST00000841804.1:n.189+11209C>T

Variant summary

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

The ENST00000841804.1(ENSG00000309511):​n.189+11209C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,984 control chromosomes in the GnomAD database, including 26,799 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 (26799 hom., cov: 31)
• Consequence: ENSG00000309511 ENST00000841804.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 31 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309511	ENST00000841804.1		n.189+11209C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85788 AN: 151866 Hom.: 26741 Cov.: 31

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.565 AC: 85892 AN: 151984 Hom.: 26799 Cov.: 31 AF XY: 0.555 AC XY: 41207 AN XY: 74262

African (AFR) AF: 0.844 AC: 35043 AN: 41504

American (AMR) AF: 0.416 AC: 6343 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1477 AN: 3466

East Asian (EAS) AF: 0.476 AC: 2454 AN: 5152

South Asian (SAS) AF: 0.481 AC: 2313 AN: 4808

European-Finnish (FIN) AF: 0.403 AC: 4248 AN: 10546

Middle Eastern (MID) AF: 0.428 AC: 124 AN: 290

European-Non Finnish (NFE) AF: 0.477 AC: 32439 AN: 67952

Other (OTH) AF: 0.522 AC: 1100 AN: 2106

Alfa AF: 0.491 Hom.: 40851

Bravo AF: 0.577

Asia WGS AF: 0.457 AC: 1590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.46
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs713587; hg19: chr2-25158281;