13-18922294-T-C

Position:

• chr13-18922294-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000231358 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC00408	NR_104118.1	n.650-4016T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000231358	ENST00000422082.4	n.678A>G		non_coding_transcript_exon_variant	4/4	3
LINC00408	ENST00000660513.1	n.339-4016T>C		intron_variant
LINC00408	ENST00000663325.1	n.475-4016T>C		intron_variant

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

Gnomad4 NFE exome AF: 0.429

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

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.463

Alfa AF: 0.520 Hom.: 41107

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1838114; hg19: chr13-19496434;