chr13-42403303-C-T

Position:

• chr13-42403303-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.352 in 151,734 control chromosomes in the GnomAD database, including 10,978 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 0.35 (10978 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.17

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.42403303C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02341	ENST00000637462.1	n.712-8593C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53259 AN: 151616 Hom.: 10953 Cov.: 33

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.352 AC: 53336 AN: 151734 Hom.: 10978 Cov.: 33 AF XY: 0.350 AC XY: 25972 AN XY: 74178

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.349

Alfa AF: 0.258 Hom.: 4930

Bravo AF: 0.377

Asia WGS AF: 0.404 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.031
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7994531; hg19: chr13-42977439;