5-120245919-A-T

Variant names:

• chr5-120245919-A-T
• rs1363439
• ENST00000514240.1:n.248-286T>A

Variant summary

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

The ENST00000514240.1(ENSG00000251293):​n.248-286T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,162 control chromosomes in the GnomAD database, including 2,645 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 0.18 (2645 hom., cov: 32)
• Consequence: ENSG00000251293 ENST00000514240.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224
• Publications: 1 publications found

Genes affected

ENSG00000251293 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514240.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251293	ENST00000514240.1	TSL:3	n.248-286T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27048 AN: 152044 Hom.: 2631 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.178 AC: 27098 AN: 152162 Hom.: 2645 Cov.: 32 AF XY: 0.182 AC XY: 13558 AN XY: 74386

African (AFR) AF: 0.198 AC: 8232 AN: 41516

American (AMR) AF: 0.231 AC: 3519 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 599 AN: 3466

East Asian (EAS) AF: 0.374 AC: 1933 AN: 5166

South Asian (SAS) AF: 0.225 AC: 1084 AN: 4826

European-Finnish (FIN) AF: 0.178 AC: 1881 AN: 10594

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9167 AN: 68010

Other (OTH) AF: 0.182 AC: 384 AN: 2114

Alfa AF: 0.160 Hom.: 246

Bravo AF: 0.189

Asia WGS AF: 0.320 AC: 1114 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.64
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1363439; hg19: chr5-119581614;