chr1-193453636-A-G

Variant names:

• chr1-193453636-A-G
• rs1324329
• ENST00000767304.1:n.236-4005A>G

Variant summary

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

The ENST00000767304.1(ENSG00000286285):​n.236-4005A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 151,902 control chromosomes in the GnomAD database, including 2,166 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 (2166 hom., cov: 32)
• Consequence: ENSG00000286285 ENST00000767304.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 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
ENSG00000286285	ENST00000767304.1	n.236-4005A>G		intron_variant	Intron 2 of 3
ENSG00000286285	ENST00000767305.1	n.105-4005A>G		intron_variant	Intron 1 of 2
ENSG00000286285	ENST00000767306.1	n.62-4005A>G		intron_variant	Intron 1 of 2
LINC01031	ENST00000767397.1	n.325-4005A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22313 AN: 151784 Hom.: 2150 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0907

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: 0.147 AC: 22367 AN: 151902 Hom.: 2166 Cov.: 32 AF XY: 0.148 AC XY: 11016 AN XY: 74242

African (AFR) AF: 0.223 AC: 9218 AN: 41414

American (AMR) AF: 0.206 AC: 3145 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 358 AN: 3466

East Asian (EAS) AF: 0.354 AC: 1818 AN: 5130

South Asian (SAS) AF: 0.139 AC: 672 AN: 4818

European-Finnish (FIN) AF: 0.0907 AC: 961 AN: 10590

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

European-Non Finnish (NFE) AF: 0.0858 AC: 5829 AN: 67930

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

Alfa AF: 0.136 Hom.: 724

Bravo AF: 0.162

Asia WGS AF: 0.214 AC: 745 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.61
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1324329; hg19: chr1-193422766; COSMIC: COSV60005630;