chr4-110796911-G-A

Variant names:

• chr4-110796911-G-A
• rs6843082
• ENST00000512794.1:n.123G>A

Variant summary

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

The ENST00000512794.1(LINC01438):​n.123G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 151,970 control chromosomes in the GnomAD database, including 38,234 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 0.70 (38230 hom., cov: 32)
  • Exomes 𝑓: 1.0 (4 hom.)
• Consequence: LINC01438 ENST00000512794.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 78 publications found

Genes affected

LINC01438 (HGNC:50757): (long intergenic non-protein coding RNA 1438)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 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
LINC01438	ENST00000512794.1	n.123G>A		non_coding_transcript_exon_variant	Exon 2 of 2	4
LINC01438	ENST00000754041.1	n.360G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106427 AN: 151846 Hom.: 38204 Cov.: 32

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.705

GnomAD4 exome AF: 1.00 AC: 8 AN: 8 Hom.: 4 Cov.: 0 AF XY: 1.00 AC XY: 6 AN XY: 6

African (AFR) AF: 1.00 AC: 4 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 4 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.701 AC: 106499 AN: 151962 Hom.: 38230 Cov.: 32 AF XY: 0.685 AC XY: 50881 AN XY: 74290

African (AFR) AF: 0.694 AC: 28742 AN: 41416

American (AMR) AF: 0.593 AC: 9037 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2160 AN: 3470

East Asian (EAS) AF: 0.262 AC: 1355 AN: 5166

South Asian (SAS) AF: 0.653 AC: 3145 AN: 4818

European-Finnish (FIN) AF: 0.679 AC: 7175 AN: 10570

Middle Eastern (MID) AF: 0.702 AC: 205 AN: 292

European-Non Finnish (NFE) AF: 0.770 AC: 52354 AN: 67960

Other (OTH) AF: 0.703 AC: 1485 AN: 2112

Alfa AF: 0.749 Hom.: 151316

Bravo AF: 0.696

Asia WGS AF: 0.497 AC: 1731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	11
DANN	Benign	0.77
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs6843082; hg19: chr4-111718067;