rs10463914

Variant names:

• chr5-134231069-G-A
• rs10463914
• ENST00000703317.1:n.*73+11823C>T

Variant summary

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

The ENST00000703317.1(ENSG00000273345):​n.*73+11823C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0986 in 152,086 control chromosomes in the GnomAD database, including 879 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 0.099 (879 hom., cov: 31)
• Consequence: ENSG00000273345 ENST00000703317.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 2 publications found

Genes affected

ENSG00000273345 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000703317.1. 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
	ENSG00000273345	ENST00000703317.1		n.*73+11823C>T		intron	N/A	ENSP00000515260.1	A0A8V8TQA6
	ENSG00000273345	ENST00000703355.1		n.1189C>T		non_coding_transcript_exon	Exon 8 of 9
	ENSG00000273345	ENST00000518409.2	TSL:2	n.905-24938C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0985 AC: 14975 AN: 151968 Hom.: 872 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.0552

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0654

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.0986 AC: 14998 AN: 152086 Hom.: 879 Cov.: 31 AF XY: 0.104 AC XY: 7748 AN XY: 74348

African (AFR) AF: 0.128 AC: 5302 AN: 41492

American (AMR) AF: 0.157 AC: 2395 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0839 AC: 291 AN: 3470

East Asian (EAS) AF: 0.0548 AC: 284 AN: 5186

South Asian (SAS) AF: 0.0986 AC: 475 AN: 4816

European-Finnish (FIN) AF: 0.140 AC: 1481 AN: 10542

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0654 AC: 4445 AN: 67978

Other (OTH) AF: 0.122 AC: 258 AN: 2114

Alfa AF: 0.0852 Hom.: 81

Bravo AF: 0.102

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.9
DANN	Benign	0.54
PhyloP100		-0.061
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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: rs10463914;

hg19: chr5-133566760;