5-102514338-C-T

Variant names:

• chr5-102514338-C-T
• rs10515328
• ENST00000797988.1:n.534+907G>A

Variant summary

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

The ENST00000797988.1(ENSG00000303908):​n.534+907G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 113,564 control chromosomes in the GnomAD database, including 4,573 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 0.24 (4573 hom., cov: 30)
• Consequence: ENSG00000303908 ENST00000797988.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 3 publications found

Genes affected

ENSG00000303908 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 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
ENSG00000303908	ENST00000797988.1	n.534+907G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.242 AC: 27438 AN: 113446 Hom.: 4562 Cov.: 30

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0188

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0930

Gnomad MID AF: 0.145

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.242 AC: 27486 AN: 113564 Hom.: 4573 Cov.: 30 AF XY: 0.237 AC XY: 12995 AN XY: 54820

African (AFR) AF: 0.474 AC: 18363 AN: 38730

American (AMR) AF: 0.161 AC: 1917 AN: 11912

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 380 AN: 2234

East Asian (EAS) AF: 0.0191 AC: 79 AN: 4132

South Asian (SAS) AF: 0.121 AC: 415 AN: 3440

European-Finnish (FIN) AF: 0.0930 AC: 510 AN: 5484

Middle Eastern (MID) AF: 0.144 AC: 31 AN: 216

European-Non Finnish (NFE) AF: 0.119 AC: 5360 AN: 45230

Other (OTH) AF: 0.213 AC: 339 AN: 1594

Alfa AF: 0.111 Hom.: 833

Bravo AF: 0.202

Asia WGS AF: 0.0940 AC: 264 AN: 2834

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.69
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10515328; hg19: chr5-101850042;