ENST00000527565.1:n.543-46970G>A

Variant names:

• chr11-7751644-C-T
• rs10500697
• ENST00000527565.1:n.543-46970G>A

Variant summary

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

The ENST00000527565.1(ENSG00000271758):​n.543-46970G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,068 control chromosomes in the GnomAD database, including 2,255 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 0.12 (2255 hom., cov: 32)
• Consequence: ENSG00000271758 ENST00000527565.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377
• Publications: 0 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 (AFR) allele frequency at 95% confidence interval = 0.309 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
ENSG00000271758	ENST00000527565.1	n.543-46970G>A		intron_variant	Intron 5 of 5	3

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17938 AN: 151952 Hom.: 2239 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0578

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.0793

Gnomad SAS AF: 0.0955

Gnomad FIN AF: 0.0222

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0367

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.118 AC: 17996 AN: 152068 Hom.: 2255 Cov.: 32 AF XY: 0.116 AC XY: 8591 AN XY: 74344

African (AFR) AF: 0.314 AC: 13015 AN: 41464

American (AMR) AF: 0.0577 AC: 881 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0752 AC: 261 AN: 3470

East Asian (EAS) AF: 0.0789 AC: 408 AN: 5174

South Asian (SAS) AF: 0.0951 AC: 458 AN: 4814

European-Finnish (FIN) AF: 0.0222 AC: 235 AN: 10582

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0367 AC: 2496 AN: 67986

Other (OTH) AF: 0.100 AC: 211 AN: 2106

Alfa AF: 0.0897 Hom.: 190

Bravo AF: 0.131

Asia WGS AF: 0.114 AC: 397 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	3.0
DANN	Benign	0.81
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs10500697; hg19: chr11-7773191;