rs1456139

Variant names:

• chr3-150923517-G-A
• rs1456139
• ENST00000562308.5:n.103+18065C>T

Variant summary

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

The ENST00000562308.5(ENSG00000260234):​n.103+18065C>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 ENST00000562308.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 3 publications found

Genes affected

ENSG00000260234 (HGNC:):

SIAH2-AS1 (HGNC:40526): (SIAH2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260234	ENST00000569170.5	n.161-16045C>T		intron_variant	Intron 1 of 10	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

African (AFR) AF: 0.750 AC: 31107 AN: 41496

American (AMR) AF: 0.476 AC: 7284 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1788 AN: 3468

East Asian (EAS) AF: 0.502 AC: 2590 AN: 5164

South Asian (SAS) AF: 0.426 AC: 2052 AN: 4814

European-Finnish (FIN) AF: 0.434 AC: 4582 AN: 10554

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25627 AN: 67990

Other (OTH) AF: 0.486 AC: 1028 AN: 2114

Alfa AF: 0.405 Hom.: 37603

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
PhyloP100		-1.9

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

Other links and lift over

dbSNP: rs1456139; hg19: chr3-150641304;