rs2508746

Variant names:

• chr11-76559906-C-T
• rs2508746
• ENST00000830356.1:n.399-4261G>A

Variant summary

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

The ENST00000830356.1(ENSG00000308001):​n.399-4261G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,918 control chromosomes in the GnomAD database, including 14,279 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 0.43 (14279 hom., cov: 31)
• Consequence: ENSG00000308001 ENST00000830356.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 9 publications found

Genes affected

ENSG00000308001 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.482 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
ENSG00000308001	ENST00000830356.1	n.399-4261G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64538 AN: 151800 Hom.: 14276 Cov.: 31

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.425 AC: 64572 AN: 151918 Hom.: 14279 Cov.: 31 AF XY: 0.419 AC XY: 31108 AN XY: 74242

African (AFR) AF: 0.377 AC: 15604 AN: 41434

American (AMR) AF: 0.341 AC: 5208 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1943 AN: 3468

East Asian (EAS) AF: 0.206 AC: 1058 AN: 5136

South Asian (SAS) AF: 0.297 AC: 1427 AN: 4810

European-Finnish (FIN) AF: 0.447 AC: 4713 AN: 10548

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.486 AC: 33053 AN: 67942

Other (OTH) AF: 0.430 AC: 906 AN: 2108

Alfa AF: 0.463 Hom.: 28452

Bravo AF: 0.418

Asia WGS AF: 0.264 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.8
DANN	Benign	0.44
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2508746; hg19: chr11-76270950;