rs10500777

Variant names:

• chr11-13254764-C-T
• rs10500777
• ENST00000787640.1:n.65+2813C>T

Variant summary

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

The ENST00000787640.1(ENSG00000302524):​n.65+2813C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,090 control chromosomes in the GnomAD database, including 1,923 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 0.15 (1923 hom., cov: 33)
• Consequence: ENSG00000302524 ENST00000787640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487
• Publications: 1 publications found

Genes affected

ENSG00000302524 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000787640.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302524	ENST00000787640.1		n.65+2813C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23371 AN: 151972 Hom.: 1919 Cov.: 33

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.154 AC: 23392 AN: 152090 Hom.: 1923 Cov.: 33 AF XY: 0.159 AC XY: 11789 AN XY: 74330

African (AFR) AF: 0.140 AC: 5815 AN: 41476

American (AMR) AF: 0.151 AC: 2308 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 636 AN: 3470

East Asian (EAS) AF: 0.223 AC: 1154 AN: 5168

South Asian (SAS) AF: 0.198 AC: 953 AN: 4818

European-Finnish (FIN) AF: 0.205 AC: 2169 AN: 10574

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9764 AN: 67990

Other (OTH) AF: 0.153 AC: 322 AN: 2108

Alfa AF: 0.148 Hom.: 216

Bravo AF: 0.151

Asia WGS AF: 0.201 AC: 698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.7
DANN	Benign	0.67
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs10500777; hg19: chr11-13276311;