5-159354596-T-C

Variant names:

• chr5-159354596-T-C
• rs6869411
• ENST00000515337.1:n.953+475T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000515337.1(ENSG00000249738):​n.953+475T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,926 control chromosomes in the GnomAD database, including 15,069 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 0.43 (15069 hom., cov: 31)
• Consequence: ENSG00000249738 ENST00000515337.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

Genes affected

ENSG00000249738 (HGNC:58156):

LOC285626 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC285626	NR_037889.1	n.953+475T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249738	ENST00000515337.1	n.953+475T>C		intron_variant	Intron 4 of 4	2
ENSG00000249738	ENST00000635333.1	n.282+475T>C		intron_variant	Intron 3 of 7	5
ENSG00000249738	ENST00000641150.1	n.532+475T>C		intron_variant	Intron 4 of 4
ENSG00000249738	ENST00000648969.1	n.53+475T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65946 AN: 151808 Hom.: 15047 Cov.: 31

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.435 AC: 66033 AN: 151926 Hom.: 15069 Cov.: 31 AF XY: 0.442 AC XY: 32810 AN XY: 74230

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.399

Alfa AF: 0.361 Hom.: 18479

Bravo AF: 0.439

Asia WGS AF: 0.436 AC: 1517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6869411; hg19: chr5-158781604;