5-135915418-T-G

Variant names:

• chr5-135915418-T-G
• rs1859428
• ENST00000523722.1:n.239+2256A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000523722.1(ENSG00000253927):​n.239+2256A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,056 control chromosomes in the GnomAD database, including 11,151 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 0.37 (11151 hom., cov: 32)
• Consequence: ENSG00000253927 ENST00000523722.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

Genes affected

ENSG00000253927 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.507 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
ENSG00000253927	ENST00000523722.1	n.239+2256A>C		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56291 AN: 151938 Hom.: 11116 Cov.: 32

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.371 AC: 56372 AN: 152056 Hom.: 11151 Cov.: 32 AF XY: 0.371 AC XY: 27536 AN XY: 74318

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.371

Alfa AF: 0.326 Hom.: 11129

Bravo AF: 0.381

Asia WGS AF: 0.356 AC: 1239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.050
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1859428; hg19: chr5-135251107;