rs10064618

Variant names:

• chr5-154392729-G-A
• rs10064618
• ENST00000524264.6:n.481C>T

Variant summary

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

The ENST00000524264.6(SAP30L-AS1):​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 0.523 in 151,876 control chromosomes in the GnomAD database, including 22,357 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 0.52 (22354 hom., cov: 31)
  • Exomes 𝑓: 0.45 (3 hom.)
• Consequence: SAP30L-AS1 ENST00000524264.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 5 publications found

Genes affected

SAP30L-AS1 (HGNC:26760): (SAP30L antisense RNA 1 (head to head))

GALNT10 (HGNC:19873): (polypeptide N-acetylgalactosaminyltransferase 10) This gene encodes a member of the GalNAc polypeptide N-acetylgalactosaminyltransferases. These enzymes catalyze the first step in the synthesis of mucin-type oligosaccharides. These proteins transfer GalNAc from UDP-GalNAc to either serine or threonine residues of polypeptide acceptors. The protein encoded by this locus may have increased catalytic activity toward glycosylated peptides compared to activity toward non-glycosylated peptides.[provided by RefSeq, Apr 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000524264.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT10	NM_198321.4	MANE Select	c.1056+6299G>A		intron	N/A	NP_938080.1
	SAP30L-AS1	NR_037897.1		n.490C>T		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAP30L-AS1	ENST00000524264.6	TSL:1	n.481C>T		non_coding_transcript_exon	Exon 3 of 3
	GALNT10	ENST00000297107.11	TSL:1 MANE Select	c.1056+6299G>A		intron	N/A	ENSP00000297107.6
	GALNT10	ENST00000377661.2	TSL:5	c.870+6299G>A		intron	N/A	ENSP00000366889.2

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79337 AN: 151736 Hom.: 22309 Cov.: 31

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.511

GnomAD4 exome AF: 0.455 AC: 10 AN: 22 Hom.: 3 Cov.: 0 AF XY: 0.455 AC XY: 10 AN XY: 22

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.438 AC: 7 AN: 16

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.523 AC: 79443 AN: 151854 Hom.: 22354 Cov.: 31 AF XY: 0.528 AC XY: 39172 AN XY: 74180

African (AFR) AF: 0.719 AC: 29763 AN: 41396

American (AMR) AF: 0.537 AC: 8199 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1416 AN: 3468

East Asian (EAS) AF: 0.649 AC: 3344 AN: 5150

South Asian (SAS) AF: 0.529 AC: 2551 AN: 4824

European-Finnish (FIN) AF: 0.513 AC: 5373 AN: 10482

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.398 AC: 27061 AN: 67942

Other (OTH) AF: 0.509 AC: 1077 AN: 2114

Alfa AF: 0.432 Hom.: 29649

Bravo AF: 0.537

Asia WGS AF: 0.617 AC: 2143 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.47
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10064618; hg19: chr5-153772289; COSMIC: COSV51723831; COSMIC: COSV51723831;