chr10-113475355-T-C

Variant names:

• chr10-113475355-T-C
• rs1472750
• ENST00000775326.1:n.361-1219T>C

Variant summary

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

The ENST00000775326.1(ENSG00000300979):​n.361-1219T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.918 in 152,216 control chromosomes in the GnomAD database, including 64,209 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 0.92 (64209 hom., cov: 31)
• Consequence: ENSG00000300979 ENST00000775326.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467
• Publications: 15 publications found

Genes affected

ENSG00000300979 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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
ENSG00000300979	ENST00000775326.1	n.361-1219T>C		intron_variant	Intron 2 of 2
ENSG00000300979	ENST00000775328.1	n.414+55T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.918 AC: 139696 AN: 152098 Hom.: 64171 Cov.: 31

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.948

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.926

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

GnomAD4 genome AF: 0.918 AC: 139786 AN: 152216 Hom.: 64209 Cov.: 31 AF XY: 0.918 AC XY: 68313 AN XY: 74400

African (AFR) AF: 0.921 AC: 38240 AN: 41510

American (AMR) AF: 0.948 AC: 14514 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3161 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5149 AN: 5178

South Asian (SAS) AF: 0.898 AC: 4319 AN: 4812

European-Finnish (FIN) AF: 0.911 AC: 9648 AN: 10596

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.908 AC: 61775 AN: 68022

Other (OTH) AF: 0.922 AC: 1951 AN: 2116

Alfa AF: 0.914 Hom.: 117369

Bravo AF: 0.922

Asia WGS AF: 0.944 AC: 3284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.42
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs1472750; hg19: chr10-115235114;