rs11188072

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 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. Variant has been reported in Lovd as Benign (no stars).

• Frequency: Genomes: 𝑓 0.20 (3313 hom., cov: 32)
• Consequence: ENSG00000276490 ENST00000464755.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.988

Genes affected

ENSG00000276490 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BP6: Variant 10-94759304-C-T is Benign according to our data. Variant chr10-94759304-C-T is described in Lovd as [Benign].
• 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

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.00946

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.200

Alfa AF: 0.200 Hom.: 610

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs11188072; hg19: chr10-96519061;