rs1478388

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr5-150918553-G-A
• chr5-150918553-G-C
• chr5-150918553-G-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901112	XR_007058999.1	n.133-234G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301073	ENST00000775956.1	n.103-234G>A		intron_variant	Intron 1 of 1

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 v4.3

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;