5-135915418-T-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

ENSG00000253927 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523722.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253927	ENST00000523722.1	TSL:3	n.239+2256A>C		intron	N/A

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

African (AFR) AF: 0.513 AC: 21268 AN: 41462

American (AMR) AF: 0.307 AC: 4697 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1667 AN: 3472

East Asian (EAS) AF: 0.394 AC: 2026 AN: 5148

South Asian (SAS) AF: 0.320 AC: 1542 AN: 4820

European-Finnish (FIN) AF: 0.293 AC: 3098 AN: 10574

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20963 AN: 67986

Other (OTH) AF: 0.371 AC: 783 AN: 2108

Alfa AF: 0.332 Hom.: 14628

Bravo AF: 0.381

Asia WGS AF: 0.356 AC: 1239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.050
DANN	Benign	0.47
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1859428; hg19: chr5-135251107;