rs9509608

Variant names:

• chr13-18724424-G-A
• rs9509608
• ENST00000446657.2:n.481C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

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
• Publications: 1 publications found

Genes affected

GXYLT1P1 (HGNC:39676): (GXYLT1 pseudogene 1)

ENSG00000301850 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BS2: High Homozygotes in GnomAd4 at 17 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GXYLT1P1		n.18724424G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GXYLT1P1	ENST00000446657.2	n.481C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000301850	ENST00000782204.1	n.77-836G>A		intron_variant	Intron 1 of 1

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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0107 AC: 29 AN: 2712

American (AMR) AF: 0.0363 AC: 174 AN: 4794

Ashkenazi Jewish (ASJ) AF: 0.0386 AC: 165 AN: 4278

East Asian (EAS) AF: 0.00 AC: 0 AN: 4978

South Asian (SAS) AF: 0.0158 AC: 461 AN: 29124

European-Finnish (FIN) AF: 0.0503 AC: 537 AN: 10680

Middle Eastern (MID) AF: 0.0444 AC: 31 AN: 698

European-Non Finnish (NFE) AF: 0.0638 AC: 6760 AN: 105998

Other (OTH) AF: 0.0472 AC: 433 AN: 9180

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0175 AC: 728 AN: 41582

American (AMR) AF: 0.0645 AC: 984 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0601 AC: 208 AN: 3462

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.0217 AC: 105 AN: 4830

European-Finnish (FIN) AF: 0.0702 AC: 740 AN: 10542

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.0885 AC: 6003 AN: 67858

Other (OTH) AF: 0.0722 AC: 152 AN: 2104

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0831 Hom.: 890

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
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs9509608; hg19: chr13-19298564;