rs538385

Positions:

• chr13-29655528-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 0.371 in 151,986 control chromosomes in the GnomAD database, including 10,877 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 0.37 (10877 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.29655528T>C		intergenic_region
LOC102723345	NR_135320.1	n.*50T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56351 AN: 151868 Hom.: 10860 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.371 AC: 56382 AN: 151986 Hom.: 10877 Cov.: 32 AF XY: 0.376 AC XY: 27918 AN XY: 74298

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.396

Alfa AF: 0.392 Hom.: 22048

Bravo AF: 0.372

Asia WGS AF: 0.371 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.072
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs538385; hg19: chr13-30229665;