ENST00000642039.2:n.718-19661G>A

Variant names:

• chr5-158568795-G-A
• rs1428445
• ENST00000642039.2:n.718-19661G>A

Variant summary

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

The ENST00000642039.2(ENSG00000254135):​n.718-19661G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,068 control chromosomes in the GnomAD database, including 5,874 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 0.27 (5874 hom., cov: 32)
• Consequence: ENSG00000254135 ENST00000642039.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25
• Publications: 4 publications found

Genes affected

ENSG00000254135 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.362 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
ENSG00000254135	ENST00000642039.2	n.718-19661G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40277 AN: 151946 Hom.: 5869 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.265 AC: 40313 AN: 152068 Hom.: 5874 Cov.: 32 AF XY: 0.262 AC XY: 19469 AN XY: 74372

African (AFR) AF: 0.367 AC: 15225 AN: 41452

American (AMR) AF: 0.294 AC: 4497 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 634 AN: 3466

East Asian (EAS) AF: 0.304 AC: 1574 AN: 5170

South Asian (SAS) AF: 0.374 AC: 1799 AN: 4814

European-Finnish (FIN) AF: 0.122 AC: 1295 AN: 10596

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14505 AN: 67974

Other (OTH) AF: 0.262 AC: 553 AN: 2110

Alfa AF: 0.233 Hom.: 2363

Bravo AF: 0.280

Asia WGS AF: 0.355 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.10
DANN	Benign	0.73
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs1428445; hg19: chr5-157995803;