1-193452230-A-G

Variant names:

• chr1-193452230-A-G
• rs7528241
• ENST00000767304.1:n.236-5411A>G

Variant summary

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

The ENST00000767304.1(ENSG00000286285):​n.236-5411A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 151,992 control chromosomes in the GnomAD database, including 2,226 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 0.15 (2226 hom., cov: 32)
• Consequence: ENSG00000286285 ENST00000767304.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257
• Publications: 5 publications found

Genes affected

ENSG00000286285 (HGNC:):

LINC01031 (HGNC:49017): (long intergenic non-protein coding RNA 1031)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767304.1. 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
	ENSG00000286285	ENST00000767304.1		n.236-5411A>G		intron	N/A
	ENSG00000286285	ENST00000767305.1		n.105-5411A>G		intron	N/A
	ENSG00000286285	ENST00000767306.1		n.62-5411A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22562 AN: 151874 Hom.: 2210 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0911

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0858

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.149 AC: 22616 AN: 151992 Hom.: 2226 Cov.: 32 AF XY: 0.150 AC XY: 11130 AN XY: 74280

African (AFR) AF: 0.228 AC: 9458 AN: 41462

American (AMR) AF: 0.207 AC: 3155 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3466

East Asian (EAS) AF: 0.354 AC: 1813 AN: 5118

South Asian (SAS) AF: 0.139 AC: 669 AN: 4822

European-Finnish (FIN) AF: 0.0911 AC: 966 AN: 10604

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0858 AC: 5832 AN: 67956

Other (OTH) AF: 0.144 AC: 304 AN: 2114

Alfa AF: 0.110 Hom.: 5323

Bravo AF: 0.164

Asia WGS AF: 0.214 AC: 745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.45
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs7528241; hg19: chr1-193421360; COSMIC: COSV60005612;