chr5-158565215-T-A

Position:

• chr5-158565215-T-A

Variant summary

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

The ENST00000642039.1(ENSG00000254135):​n.705-23241T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,056 control chromosomes in the GnomAD database, including 4,823 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 0.24 (4823 hom., cov: 32)
• Consequence: ENST00000642039.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.857

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000642039.1	n.705-23241T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37033 AN: 151936 Hom.: 4816 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.244 AC: 37068 AN: 152056 Hom.: 4823 Cov.: 32 AF XY: 0.243 AC XY: 18072 AN XY: 74346

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.241

Alfa AF: 0.123 Hom.: 195

Bravo AF: 0.255

Asia WGS AF: 0.333 AC: 1161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs890945; hg19: chr5-157992223;