5-107704741-C-T

Variant names:

• chr5-107704741-C-T
• rs12654281
• ENST00000502287.1:n.434-2434G>A

Variant summary

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

The ENST00000502287.1(ENSG00000249959):​n.434-2434G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,858 control chromosomes in the GnomAD database, including 9,691 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 0.34 (9691 hom., cov: 31)
• Consequence: ENSG00000249959 ENST00000502287.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.850
• Publications: 7 publications found

Genes affected

ENSG00000249959 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.524 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
ENSG00000249959	ENST00000502287.1	n.434-2434G>A		intron_variant	Intron 3 of 4	5
ENSG00000249959	ENST00000509458.5	n.322+461G>A		intron_variant	Intron 3 of 4	3
ENSG00000249959	ENST00000653896.1	n.130+461G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51246 AN: 151738 Hom.: 9688 Cov.: 31

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.338 AC: 51258 AN: 151858 Hom.: 9691 Cov.: 31 AF XY: 0.340 AC XY: 25215 AN XY: 74204

African (AFR) AF: 0.159 AC: 6593 AN: 41410

American (AMR) AF: 0.400 AC: 6091 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1393 AN: 3468

East Asian (EAS) AF: 0.374 AC: 1927 AN: 5156

South Asian (SAS) AF: 0.541 AC: 2600 AN: 4806

European-Finnish (FIN) AF: 0.366 AC: 3863 AN: 10546

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27560 AN: 67912

Other (OTH) AF: 0.342 AC: 724 AN: 2114

Alfa AF: 0.376 Hom.: 8502

Bravo AF: 0.329

Asia WGS AF: 0.387 AC: 1348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	4.4
DANN	Benign	0.84
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs12654281; hg19: chr5-107040442;