rs890945

Variant names:

• chr5-158565215-T-A
• rs890945
• ENST00000642039.1:n.705-23241T>A

Your query was ambiguous. Multiple possible variants found:

• chr5-158565215-T-A
• chr5-158565215-T-G

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 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: ENSG00000254135 ENST00000642039.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.857

Genes affected

ENSG00000254135 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254135	ENST00000642039.1	n.705-23241T>A		intron_variant	Intron 3 of 3

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;