rs11199874

Variant names:

• chr10-121273005-G-A
• rs11199874
• ENST00000718585.1:n.66+12400C>T

Variant summary

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

The ENST00000718585.1(ENSG00000293725):​n.66+12400C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,084 control chromosomes in the GnomAD database, including 4,206 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 0.23 (4206 hom., cov: 32)
• Consequence: ENSG00000293725 ENST00000718585.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 34 publications found

Genes affected

ENSG00000293725 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378523	XR_007062321.1	n.515+40211C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293725	ENST00000718585.1	n.66+12400C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34723 AN: 151966 Hom.: 4204 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.228 AC: 34730 AN: 152084 Hom.: 4206 Cov.: 32 AF XY: 0.229 AC XY: 17054 AN XY: 74346

African (AFR) AF: 0.142 AC: 5893 AN: 41510

American (AMR) AF: 0.266 AC: 4068 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1177 AN: 3470

East Asian (EAS) AF: 0.260 AC: 1337 AN: 5142

South Asian (SAS) AF: 0.163 AC: 785 AN: 4812

European-Finnish (FIN) AF: 0.312 AC: 3298 AN: 10584

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17251 AN: 67980

Other (OTH) AF: 0.253 AC: 534 AN: 2108

Alfa AF: 0.244 Hom.: 12972

Bravo AF: 0.225

Asia WGS AF: 0.193 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.098
DANN	Benign	0.48
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs11199874; hg19: chr10-123032519;