rs1478388

chr5-150918553-G-Achr5-150918553-G-Cchr5-150918553-G-T

Variant summary

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

The XR_007058999.1(LOC124901112):n.133-234G>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 0.576 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: LOC124901112 XR_007058999.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

Genes affected

LOC124901112 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124901112	XR_007058999.1	n.133-234G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.723

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.817

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.587

Alfa AF: 0.545 Hom.: 4007

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1478388; hg19: chr5-150298115;