rs6691259

chr1-59144935-A-G

Variant summary

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

The NR_027120.1(HSD52):n.132+1741T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,216 control chromosomes in the GnomAD database, including 2,694 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 0.14 (2694 hom., cov: 33)
• Consequence: HSD52 NR_027120.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248

Genes affected

FGGY-DT (HGNC:55265): (FGGY divergent transcript)

HSD52 (HGNC:):

LINC01358 (HGNC:50589): (long intergenic non-protein coding RNA 1358)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSD52	NR_027120.1	n.132+1741T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGGY-DT	ENST00000647858.1	n.1955-11605T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20844 AN: 152098 Hom.: 2685 Cov.: 33

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0883

Gnomad ASJ AF: 0.0735

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0468

Gnomad FIN AF: 0.0362

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0604

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.137 AC: 20893 AN: 152216 Hom.: 2694 Cov.: 33 AF XY: 0.132 AC XY: 9847 AN XY: 74432

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.0881

Gnomad4 ASJ AF: 0.0735

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0471

Gnomad4 FIN AF: 0.0362

Gnomad4 NFE AF: 0.0605

Gnomad4 OTH AF: 0.112

Alfa AF: 0.105 Hom.: 205

Bravo AF: 0.149

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.6
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6691259; hg19: chr1-59610607;