rs2008801

Variant names:

• chr11-115137455-G-T
• rs2008801
• ENST00000796160.1:n.277+2319C>A

Variant summary

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

The ENST00000796160.1(ENSG00000303624):​n.277+2319C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,162 control chromosomes in the GnomAD database, including 3,717 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 0.20 (3717 hom., cov: 32)
• Consequence: ENSG00000303624 ENST00000796160.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.397
• Publications: 8 publications found

Genes affected

ENSG00000303624 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.368 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
ENSG00000303624	ENST00000796160.1	n.277+2319C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30256 AN: 152044 Hom.: 3710 Cov.: 32

Gnomad AFR AF: 0.0699

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.199 AC: 30267 AN: 152162 Hom.: 3717 Cov.: 32 AF XY: 0.203 AC XY: 15127 AN XY: 74364

African (AFR) AF: 0.0698 AC: 2901 AN: 41552

American (AMR) AF: 0.247 AC: 3781 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 519 AN: 3470

East Asian (EAS) AF: 0.129 AC: 667 AN: 5164

South Asian (SAS) AF: 0.383 AC: 1844 AN: 4820

European-Finnish (FIN) AF: 0.286 AC: 3029 AN: 10574

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.250 AC: 16978 AN: 67990

Other (OTH) AF: 0.201 AC: 424 AN: 2110

Alfa AF: 0.235 Hom.: 7546

Bravo AF: 0.185

Asia WGS AF: 0.238 AC: 829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.54
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs2008801; hg19: chr11-115008175;