rs10788575

Variant names:

• chr10-88008827-G-A
• rs10788575
• ENST00000752269.1:n.191+15767G>A

Variant summary

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

The ENST00000752269.1(ENSG00000297977):​n.191+15767G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,194 control chromosomes in the GnomAD database, including 1,813 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 0.14 (1813 hom., cov: 32)
• Consequence: ENSG00000297977 ENST00000752269.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 17 publications found

Genes affected

ENSG00000297977 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 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
ENSG00000297977	ENST00000752269.1	n.191+15767G>A		intron_variant	Intron 2 of 2
ENSG00000297977	ENST00000752273.1	n.112-26472G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21181 AN: 152076 Hom.: 1804 Cov.: 32

Gnomad AFR AF: 0.0855

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.139 AC: 21212 AN: 152194 Hom.: 1813 Cov.: 32 AF XY: 0.140 AC XY: 10392 AN XY: 74382

African (AFR) AF: 0.0859 AC: 3569 AN: 41546

American (AMR) AF: 0.210 AC: 3199 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3468

East Asian (EAS) AF: 0.399 AC: 2065 AN: 5176

South Asian (SAS) AF: 0.124 AC: 596 AN: 4820

European-Finnish (FIN) AF: 0.107 AC: 1137 AN: 10594

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9798 AN: 68010

Other (OTH) AF: 0.148 AC: 312 AN: 2110

Alfa AF: 0.144 Hom.: 2665

Bravo AF: 0.147

Asia WGS AF: 0.237 AC: 825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.4
DANN	Benign	0.46
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs10788575; hg19: chr10-89768584;