rs10500647

Variant names:

• chr11-5539485-C-A
• rs10500647
• ENST00000380259.7:n.*739+51340G>T

Variant summary

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

The ENST00000380259.7(ENSG00000239920):​n.*739+51340G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0914 in 137,722 control chromosomes in the GnomAD database, including 1,134 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 0.091 (1134 hom., cov: 26)
• Consequence: ENSG00000239920 ENST00000380259.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• Publications: 2 publications found

Genes affected

ENSG00000239920 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000380259.7. 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
	ENSG00000239920	ENST00000380259.7	TSL:5	n.*739+51340G>T		intron	N/A	ENSP00000369609.3	A0A2U3TZJ3

Frequencies

GnomAD3 genomes AF: 0.0913 AC: 12572 AN: 137652 Hom.: 1133 Cov.: 26

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.0268

Gnomad AMR AF: 0.0961

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0573

Gnomad MID AF: 0.0912

Gnomad NFE AF: 0.0173

Gnomad OTH AF: 0.0781

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

GnomAD4 genome AF: 0.0914 AC: 12593 AN: 137722 Hom.: 1134 Cov.: 26 AF XY: 0.0964 AC XY: 6396 AN XY: 66370

African (AFR) AF: 0.185 AC: 6881 AN: 37206

American (AMR) AF: 0.0961 AC: 1306 AN: 13586

Ashkenazi Jewish (ASJ) AF: 0.0406 AC: 134 AN: 3298

East Asian (EAS) AF: 0.386 AC: 1910 AN: 4944

South Asian (SAS) AF: 0.145 AC: 614 AN: 4236

European-Finnish (FIN) AF: 0.0573 AC: 453 AN: 7910

Middle Eastern (MID) AF: 0.0938 AC: 24 AN: 256

European-Non Finnish (NFE) AF: 0.0173 AC: 1099 AN: 63556

Other (OTH) AF: 0.0796 AC: 149 AN: 1872

Alfa AF: 0.0538 Hom.: 62

Bravo AF: 0.0996

Asia WGS AF: 0.252 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.52
PhyloP100		-0.81
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10500647;

hg19: chr11-5560715;