5-159402519-A-T

Variant names:

• chr5-159402519-A-T
• rs12188300
• ENST00000635333.1:n.327+9942A>T

Variant summary

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

The ENST00000635333.1(ENSG00000249738):​n.327+9942A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0533 in 152,212 control chromosomes in the GnomAD database, including 298 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 0.053 (298 hom., cov: 32)
• Consequence: ENSG00000249738 ENST00000635333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346
• Publications: 55 publications found

Genes affected

ENSG00000249738 (HGNC:58156):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0848 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
ENSG00000249738	ENST00000635333.1	n.327+9942A>T		intron_variant	Intron 4 of 7	5
ENSG00000249738	ENST00000641150.1	n.533-14005A>T		intron_variant	Intron 4 of 4
ENSG00000249738	ENST00000648969.1	n.54-14005A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0533 AC: 8114 AN: 152094 Hom.: 298 Cov.: 32

Gnomad AFR AF: 0.0156

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.0426

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0164

Gnomad FIN AF: 0.0480

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0866

Gnomad OTH AF: 0.0374

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

GnomAD4 genome AF: 0.0533 AC: 8114 AN: 152212 Hom.: 298 Cov.: 32 AF XY: 0.0505 AC XY: 3755 AN XY: 74410

African (AFR) AF: 0.0156 AC: 648 AN: 41540

American (AMR) AF: 0.0425 AC: 650 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0524 AC: 182 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.0166 AC: 80 AN: 4824

European-Finnish (FIN) AF: 0.0480 AC: 508 AN: 10590

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0866 AC: 5891 AN: 68000

Other (OTH) AF: 0.0365 AC: 77 AN: 2110

Alfa AF: 0.0716 Hom.: 282

Bravo AF: 0.0506

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.6
DANN	Benign	0.71
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs12188300; hg19: chr5-158829527;