rs6691259

Variant names:

• chr1-59144935-A-G
• rs6691259
• ENST00000425914.7:n.259+1741T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000425914.7(FGGY-DT):​n.259+1741T>C variant causes a intron 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: FGGY-DT ENST00000425914.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248
• Publications: 2 publications found

Genes affected

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

JUN-DT (HGNC:49450): (JUN divergent transcript)

HSD52 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
HSD52	NR_027120.1	n.132+1741T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGGY-DT	ENST00000425914.7	n.259+1741T>C		intron_variant	Intron 1 of 2	2
FGGY-DT	ENST00000436225.2	n.440-11605T>C		intron_variant	Intron 1 of 2	3
FGGY-DT	ENST00000585367.7	n.163+1741T>C		intron_variant	Intron 1 of 2	5

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

African (AFR) AF: 0.343 AC: 14245 AN: 41482

American (AMR) AF: 0.0881 AC: 1348 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0735 AC: 255 AN: 3468

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5190

South Asian (SAS) AF: 0.0471 AC: 227 AN: 4822

European-Finnish (FIN) AF: 0.0362 AC: 384 AN: 10616

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0605 AC: 4113 AN: 68016

Other (OTH) AF: 0.112 AC: 236 AN: 2114

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
PhyloP100		0.25
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6691259; hg19: chr1-59610607;