11-7882691-T-C

Variant names:

• chr11-7882691-T-C
• rs10769846
• ENST00000527565.1:n.88+169A>G

Variant summary

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

The ENST00000527565.1(ENSG00000271758):​n.88+169A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 151,948 control chromosomes in the GnomAD database, including 39,189 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 0.72 (39189 hom., cov: 31)
• Consequence: ENSG00000271758 ENST00000527565.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.732
• Publications: 1 publications found

Genes affected

ENSG00000271758 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC283299	NR_036678.1	n.427+169A>G		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000271758	ENST00000527565.1	n.88+169A>G		intron_variant	Intron 1 of 5	3
ENSG00000254951	ENST00000527847.5	n.427+169A>G		intron_variant	Intron 2 of 7	2
ENSG00000254951	ENST00000529488.5	n.123+169A>G		intron_variant	Intron 1 of 5	5
ENSG00000254951	ENST00000533634.1	n.123+169A>G		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108818 AN: 151830 Hom.: 39156 Cov.: 31

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.717 AC: 108902 AN: 151948 Hom.: 39189 Cov.: 31 AF XY: 0.718 AC XY: 53323 AN XY: 74254

African (AFR) AF: 0.654 AC: 27041 AN: 41378

American (AMR) AF: 0.719 AC: 10977 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2652 AN: 3472

East Asian (EAS) AF: 0.842 AC: 4354 AN: 5170

South Asian (SAS) AF: 0.734 AC: 3538 AN: 4818

European-Finnish (FIN) AF: 0.751 AC: 7936 AN: 10562

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 49982 AN: 67974

Other (OTH) AF: 0.713 AC: 1503 AN: 2108

Alfa AF: 0.718 Hom.: 9892

Bravo AF: 0.712

Asia WGS AF: 0.792 AC: 2752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.69
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs10769846; hg19: chr11-7904238;