5-150918553-G-A

Variant names:

• chr5-150918553-G-A
• rs1478388
• ENST00000775956.1:n.103-234G>A

Variant summary

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

The ENST00000775956.1(ENSG00000301073):​n.103-234G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 151,964 control chromosomes in the GnomAD database, including 26,633 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 0.58 (26633 hom., cov: 32)
• Consequence: ENSG00000301073 ENST00000775956.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 5 publications found

Genes affected

ENSG00000301073 (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 (EAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775956.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301073	ENST00000775956.1		n.103-234G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87417 AN: 151844 Hom.: 26569 Cov.: 32

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.576 AC: 87543 AN: 151964 Hom.: 26633 Cov.: 32 AF XY: 0.582 AC XY: 43204 AN XY: 74276

African (AFR) AF: 0.723 AC: 30011 AN: 41484

American (AMR) AF: 0.661 AC: 10102 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2079 AN: 3466

East Asian (EAS) AF: 0.817 AC: 4222 AN: 5170

South Asian (SAS) AF: 0.627 AC: 3017 AN: 4812

European-Finnish (FIN) AF: 0.454 AC: 4782 AN: 10536

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31422 AN: 67910

Other (OTH) AF: 0.587 AC: 1239 AN: 2110

Alfa AF: 0.550 Hom.: 4205

Bravo AF: 0.599

Asia WGS AF: 0.751 AC: 2613 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	7.3
DANN	Benign	0.85
PhyloP100		-0.099

Splicing

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

Other links and lift over

dbSNP: rs1478388; hg19: chr5-150298115;