rs10517287

Variant names:

• chr4-33623080-G-T
• rs10517287
• ENST00000673514.1:n.1364+33784G>T

Variant summary

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

The ENST00000673514.1(ENSG00000288321):​n.1364+33784G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,126 control chromosomes in the GnomAD database, including 2,312 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 0.13 (2312 hom., cov: 32)
• Consequence: ENSG00000288321 ENST00000673514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 5 publications found

Genes affected

ENSG00000288321 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000673514.1. 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
	ENSG00000288321	ENST00000673514.1		n.1364+33784G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19714 AN: 152008 Hom.: 2287 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.0628

Gnomad EAS AF: 0.0715

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0456

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0373

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.130 AC: 19793 AN: 152126 Hom.: 2312 Cov.: 32 AF XY: 0.130 AC XY: 9674 AN XY: 74382

African (AFR) AF: 0.298 AC: 12372 AN: 41504

American (AMR) AF: 0.189 AC: 2879 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0628 AC: 218 AN: 3470

East Asian (EAS) AF: 0.0716 AC: 370 AN: 5166

South Asian (SAS) AF: 0.109 AC: 524 AN: 4822

European-Finnish (FIN) AF: 0.0456 AC: 484 AN: 10608

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0373 AC: 2534 AN: 67976

Other (OTH) AF: 0.122 AC: 258 AN: 2108

Alfa AF: 0.0566 Hom.: 1138

Bravo AF: 0.151

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.038
DANN	Benign	0.13
PhyloP100		-1.8

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: rs10517287;

hg19: chr4-33624702;