rs11188072

Variant names:

• chr10-94759304-C-T
• rs11188072
• ENST00000464755.1:n.932-15754C>T

Variant summary

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

The ENST00000464755.1(ENSG00000276490):​n.932-15754C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 151,974 control chromosomes in the GnomAD database, including 3,313 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 (3313 hom., cov: 32)
• Consequence: ENSG00000276490 ENST00000464755.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.988
• Publications: 23 publications found

Genes affected

ENSG00000276490 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 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
ENSG00000276490	ENST00000464755.1	n.932-15754C>T		intron_variant	Intron 6 of 13	2		ENSP00000483243.1

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30622 AN: 151856 Hom.: 3312 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.00944

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.202 AC: 30624 AN: 151974 Hom.: 3313 Cov.: 32 AF XY: 0.198 AC XY: 14707 AN XY: 74278

African (AFR) AF: 0.226 AC: 9393 AN: 41474

American (AMR) AF: 0.134 AC: 2042 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 737 AN: 3464

East Asian (EAS) AF: 0.00946 AC: 49 AN: 5178

South Asian (SAS) AF: 0.163 AC: 783 AN: 4816

European-Finnish (FIN) AF: 0.186 AC: 1950 AN: 10508

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14939 AN: 67938

Other (OTH) AF: 0.200 AC: 422 AN: 2108

Alfa AF: 0.209 Hom.: 5824

Bravo AF: 0.198

Asia WGS AF: 0.0850 AC: 295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.25
DANN	Benign	0.37
PhyloP100		-0.99

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11188072; hg19: chr10-96519061;