rs9509608

Positions:

• chr13-18724424-G-A
• chr13-18724424-G-C

Variant summary

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

The ENST00000446657.2(GXYLT1P1):​n.481C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0542 in 324,460 control chromosomes in the GnomAD database, including 34 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 0.059 (17 hom., cov: 49)
  • Exomes 𝑓: 0.050 (17 hom.)
• Consequence: GXYLT1P1 ENST00000446657.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

Genes affected

GXYLT1P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GXYLT1P1		n.18724424G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GXYLT1P1	ENST00000446657.2	n.481C>T		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.0592 AC: 8989 AN: 151900 Hom.: 17 Cov.: 49

Gnomad AFR AF: 0.0176

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0646

Gnomad ASJ AF: 0.0601

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0211

Gnomad FIN AF: 0.0702

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0884

Gnomad OTH AF: 0.0730

GnomAD4 exome AF: 0.0498 AC: 8590 AN: 172442 Hom.: 17 Cov.: 0 AF XY: 0.0455 AC XY: 4565 AN XY: 100244

Gnomad4 AFR exome AF: 0.0107

Gnomad4 AMR exome AF: 0.0363

Gnomad4 ASJ exome AF: 0.0386

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0158

Gnomad4 FIN exome AF: 0.0503

Gnomad4 NFE exome AF: 0.0638

Gnomad4 OTH exome AF: 0.0472

GnomAD4 genome AF: 0.0591 AC: 8991 AN: 152018 Hom.: 17 Cov.: 49 AF XY: 0.0578 AC XY: 4295 AN XY: 74304

Gnomad4 AFR AF: 0.0175

Gnomad4 AMR AF: 0.0645

Gnomad4 ASJ AF: 0.0601

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0217

Gnomad4 FIN AF: 0.0702

Gnomad4 NFE AF: 0.0885

Gnomad4 OTH AF: 0.0722

Alfa AF: 0.0838 Hom.: 559

Asia WGS AF: 0.0100 AC: 37 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9509608; hg19: chr13-19298564;