chr5-151930637-A-G

Variant names:

• chr5-151930637-A-G
• rs2059121
• ENST00000719159.1:n.126+3399A>G

Variant summary

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

The ENST00000719159.1(ENSG00000293808):​n.126+3399A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 152,074 control chromosomes in the GnomAD database, including 40,435 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 0.72 (40435 hom., cov: 32)
• Consequence: ENSG00000293808 ENST00000719159.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 1 publications found

Genes affected

ENSG00000293808 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000719159.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293808	ENST00000719159.1		n.126+3399A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109400 AN: 151956 Hom.: 40379 Cov.: 32

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.720 AC: 109513 AN: 152074 Hom.: 40435 Cov.: 32 AF XY: 0.714 AC XY: 53082 AN XY: 74330

African (AFR) AF: 0.899 AC: 37336 AN: 41524

American (AMR) AF: 0.689 AC: 10541 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2334 AN: 3472

East Asian (EAS) AF: 0.672 AC: 3477 AN: 5172

South Asian (SAS) AF: 0.610 AC: 2940 AN: 4822

European-Finnish (FIN) AF: 0.566 AC: 5964 AN: 10544

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44618 AN: 67938

Other (OTH) AF: 0.698 AC: 1471 AN: 2108

Alfa AF: 0.671 Hom.: 20076

Bravo AF: 0.740

Asia WGS AF: 0.662 AC: 2303 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.33
DANN	Benign	0.69
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2059121; hg19: chr5-151310198; COSMIC: COSV60212069;