chr13-18922294-T-C

Variant names:

• chr13-18922294-T-C
• rs1838114
• ENST00000422082.4:n.678A>G

Variant summary

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

The ENST00000422082.4(ENSG00000231358):​n.678A>G 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 0.435 in 152,052 control chromosomes in the GnomAD database, including 15,834 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 0.43 (15832 hom., cov: 33)
  • Exomes 𝑓: 0.50 (2 hom.)
• Consequence: ENSG00000231358 ENST00000422082.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 5 publications found

Genes affected

ENSG00000231358 (HGNC:):

LINC00408 (HGNC:42740): (long intergenic non-protein coding RNA 408)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00408	NR_104118.1	n.650-4016T>C		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231358	ENST00000422082.4	n.678A>G		non_coding_transcript_exon_variant	Exon 4 of 4	3
ENSG00000231358	ENST00000761688.1	n.490A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LINC00408	ENST00000660513.2	n.339-4016T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66066 AN: 151918 Hom.: 15837 Cov.: 33

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.463

GnomAD4 exome AF: 0.500 AC: 8 AN: 16 Hom.: 2 Cov.: 0 AF XY: 0.600 AC XY: 6 AN XY: 10

African (AFR) AC: 0 AN: 0

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) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.429 AC: 6 AN: 14

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.435 AC: 66085 AN: 152036 Hom.: 15832 Cov.: 33 AF XY: 0.433 AC XY: 32171 AN XY: 74292

African (AFR) AF: 0.243 AC: 10087 AN: 41494

American (AMR) AF: 0.443 AC: 6762 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1853 AN: 3468

East Asian (EAS) AF: 0.183 AC: 945 AN: 5176

South Asian (SAS) AF: 0.508 AC: 2448 AN: 4820

European-Finnish (FIN) AF: 0.522 AC: 5502 AN: 10538

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36891 AN: 67966

Other (OTH) AF: 0.463 AC: 976 AN: 2110

Alfa AF: 0.509 Hom.: 57495

Bravo AF: 0.417

Asia WGS AF: 0.369 AC: 1285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.49
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs1838114; hg19: chr13-19496434;