5-132059045-C-T

Variant names:

• chr5-132059045-C-T
• rs2073506
• ENST00000791953.1:n.86-3152G>A

Variant summary

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

The ENST00000791953.1(ENSG00000303119):​n.86-3152G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0718 in 152,268 control chromosomes in the GnomAD database, including 541 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 0.072 (541 hom., cov: 32)
• Consequence: ENSG00000303119 ENST00000791953.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678
• Publications: 13 publications found

Genes affected

ENSG00000303119 (HGNC:59130):

LOC105379174 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791953.1. 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
	ENSG00000303119	ENST00000791953.1		n.86-3152G>A		intron	N/A
	ENSG00000303119	ENST00000791954.1		n.248+2426G>A		intron	N/A
	ENSG00000303119	ENST00000791955.1		n.236+2426G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0718 AC: 10930 AN: 152150 Hom.: 542 Cov.: 32

Gnomad AFR AF: 0.0156

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0455

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.0650

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0914

Gnomad OTH AF: 0.0608

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

GnomAD4 genome AF: 0.0718 AC: 10927 AN: 152268 Hom.: 541 Cov.: 32 AF XY: 0.0738 AC XY: 5496 AN XY: 74440

African (AFR) AF: 0.0155 AC: 646 AN: 41558

American (AMR) AF: 0.0455 AC: 696 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3472

East Asian (EAS) AF: 0.188 AC: 971 AN: 5166

South Asian (SAS) AF: 0.0651 AC: 314 AN: 4826

European-Finnish (FIN) AF: 0.141 AC: 1491 AN: 10608

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0914 AC: 6219 AN: 68014

Other (OTH) AF: 0.0611 AC: 129 AN: 2112

Alfa AF: 0.0787 Hom.: 867

Bravo AF: 0.0624

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.5
DANN	Benign	0.48
PhyloP100		-0.68

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: rs2073506;

hg19: chr5-131394738;