rs1156387

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000251574 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503650.1. 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
	ENSG00000251574	ENST00000503650.1	TSL:3	n.329-105295G>T		intron	N/A
	ENSG00000251574	ENST00000524336.5	TSL:3	n.191-206565G>T		intron	N/A
	ENSG00000251574	ENST00000671304.1		n.283-46921G>T		intron	N/A

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

African (AFR) AF: 0.443 AC: 18341 AN: 41422

American (AMR) AF: 0.239 AC: 3650 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 980 AN: 3472

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5164

South Asian (SAS) AF: 0.225 AC: 1088 AN: 4830

European-Finnish (FIN) AF: 0.264 AC: 2790 AN: 10572

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20209 AN: 67952

Other (OTH) AF: 0.286 AC: 603 AN: 2110

Alfa AF: 0.316 Hom.: 1075

Bravo AF: 0.319

Asia WGS AF: 0.152 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.6
DANN	Benign	0.53
PhyloP100		0.81

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: rs1156387;

hg19: chr5-103925648;