5-150954136-A-T

Variant names:

• chr5-150954136-A-T
• rs931058
• ENST00000801127.1:n.460-10264T>A

Variant summary

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

The ENST00000801127.1(ENSG00000291115):​n.460-10264T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.095 in 152,274 control chromosomes in the GnomAD database, including 1,007 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 0.095 (1007 hom., cov: 32)
• Consequence: ENSG00000291115 ENST00000801127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 11 publications found

Genes affected

ENSG00000291115 (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 (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000801127.1. 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
	ENSG00000291115	ENST00000801127.1		n.460-10264T>A		intron	N/A
	ENSG00000291115	ENST00000801128.1		n.108-10264T>A		intron	N/A
	ENSG00000291115	ENST00000801129.1		n.192-10264T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0951 AC: 14465 AN: 152156 Hom.: 1007 Cov.: 32

Gnomad AFR AF: 0.0839

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0989

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0806

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.0733

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.0950 AC: 14460 AN: 152274 Hom.: 1007 Cov.: 32 AF XY: 0.0976 AC XY: 7270 AN XY: 74450

African (AFR) AF: 0.0838 AC: 3481 AN: 41550

American (AMR) AF: 0.0987 AC: 1509 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 545 AN: 3468

East Asian (EAS) AF: 0.410 AC: 2121 AN: 5178

South Asian (SAS) AF: 0.127 AC: 612 AN: 4826

European-Finnish (FIN) AF: 0.0806 AC: 855 AN: 10612

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.0733 AC: 4989 AN: 68030

Other (OTH) AF: 0.122 AC: 258 AN: 2114

Alfa AF: 0.0296 Hom.: 20

Bravo AF: 0.0994

Asia WGS AF: 0.226 AC: 786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.9
DANN	Benign	0.38
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs931058; hg19: chr5-150333698;