rs1456139

Positions:

• chr3-150923517-G-A

Variant summary

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

The ENST00000569170.5(ENSG00000260234):​n.161-16045C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 152,092 control chromosomes in the GnomAD database, including 21,237 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 0.50 (21237 hom., cov: 32)
• Consequence: ENSG00000260234 ENST00000569170.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

Genes affected

ENSG00000260234 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.150923517G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000260234	ENST00000569170.5	n.161-16045C>T		intron_variant		1		ENSP00000457784.1

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76415 AN: 151974 Hom.: 21198 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.503 AC: 76510 AN: 152092 Hom.: 21237 Cov.: 32 AF XY: 0.503 AC XY: 37380 AN XY: 74332

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.486

Alfa AF: 0.396 Hom.: 24449

Bravo AF: 0.518

Asia WGS AF: 0.465 AC: 1618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.074
DANN	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1456139; hg19: chr3-150641304;