chr1-843942-A-G

Variant names:

• chr1-843942-A-G
• rs4040617
• ENST00000445118.7:n.281-7985A>G

Variant summary

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

The ENST00000445118.7(LINC01128):​n.281-7985A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,136 control chromosomes in the GnomAD database, including 5,324 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 0.23 (5324 hom., cov: 33)
• Consequence: LINC01128 ENST00000445118.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470
• Publications: 5 publications found

Genes affected

LINC01128 (HGNC:49377): (long intergenic non-protein coding RNA 1128)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01128	NR_047519.1	n.288-3712A>G		intron_variant	Intron 2 of 5
LINC01128	NR_047521.1	n.288-7985A>G		intron_variant	Intron 2 of 4
LINC01128	NR_047523.1	n.288-7985A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01128	ENST00000445118.7	n.281-7985A>G		intron_variant	Intron 2 of 4	1
LINC01128	ENST00000449005.8	n.269-3712A>G		intron_variant	Intron 2 of 4	1
LINC01128	ENST00000669922.2	n.3081A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34768 AN: 152020 Hom.: 5313 Cov.: 33

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.229 AC: 34814 AN: 152136 Hom.: 5324 Cov.: 33 AF XY: 0.229 AC XY: 17029 AN XY: 74378

African (AFR) AF: 0.434 AC: 17992 AN: 41494

American (AMR) AF: 0.179 AC: 2730 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 522 AN: 3468

East Asian (EAS) AF: 0.105 AC: 543 AN: 5168

South Asian (SAS) AF: 0.180 AC: 868 AN: 4818

European-Finnish (FIN) AF: 0.193 AC: 2040 AN: 10596

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9445 AN: 67986

Other (OTH) AF: 0.195 AC: 411 AN: 2108

Alfa AF: 0.174 Hom.: 1314

Bravo AF: 0.234

Asia WGS AF: 0.170 AC: 590 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	1.4
DANN	Benign	0.53
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs4040617; hg19: chr1-779322;