13-42346817-T-C

Position:

• chr13-42346817-T-C

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 0.279 in 152,176 control chromosomes in the GnomAD database, including 6,609 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 0.28 (6609 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.42346817T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02341	ENST00000637462.1	n.229+4215T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42475 AN: 152058 Hom.: 6609 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.279 AC: 42475 AN: 152176 Hom.: 6609 Cov.: 32 AF XY: 0.279 AC XY: 20773 AN XY: 74406

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.260

Alfa AF: 0.310 Hom.: 4799

Bravo AF: 0.266

Asia WGS AF: 0.212 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs912100; hg19: chr13-42920953;