rs1156387

Variant names:

• chr5-104589947-C-A
• rs1156387
• ENST00000503650.1:n.329-105295G>T

Variant summary

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

The ENST00000503650.1(ENSG00000251574):​n.329-105295G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,984 control chromosomes in the GnomAD database, including 8,371 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 0.32 (8371 hom., cov: 32)
• Consequence: ENSG00000251574 ENST00000503650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.808

Genes affected

ENSG00000251574 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 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
ENSG00000251574	ENST00000503650.1	n.329-105295G>T		intron_variant	Intron 2 of 2	3
ENSG00000251574	ENST00000524336.5	n.191-206565G>T		intron_variant	Intron 2 of 2	3
ENSG00000251574	ENST00000671304.1	n.283-46921G>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47946 AN: 151866 Hom.: 8361 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.316 AC: 47994 AN: 151984 Hom.: 8371 Cov.: 32 AF XY: 0.310 AC XY: 23024 AN XY: 74292

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.286

Alfa AF: 0.311 Hom.: 992

Bravo AF: 0.319

Asia WGS AF: 0.152 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.6
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1156387; hg19: chr5-103925648;