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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446657.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GXYLT1P1	ENST00000446657.2	TSL:6	n.481C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000301850	ENST00000782204.1		n.77-836G>A		intron	N/A

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 v4.9

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;