rs1975350

chr16-30200833-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_177552.4(SULT1A3):c.105A>G(p.Gln35=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. 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 0.40 (2685 hom., cov: 6)
  • Exomes 𝑓: 0.36 (11172 hom.)
• Consequence: SULT1A3 NM_177552.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

Genes affected

SULT1A3 (HGNC:11455): (sulfotransferase family 1A member 3) Sulfotransferase enzymes catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs, and xenobiotic compounds. These cytosolic enzymes are different in their tissue distributions and substrate specificities. The gene structure (number and length of exons) is similar among family members. This gene encodes a phenol sulfotransferase with thermolabile enzyme activity. Four sulfotransferase genes are located on the p arm of chromosome 16; this gene and SULT1A4 arose from a segmental duplication. This gene is the most centromeric of the four sulfotransferase genes. Read-through transcription exists between this gene and the upstream SLX1A (SLX1 structure-specific endonuclease subunit homolog A) gene that encodes a protein containing GIY-YIG domains. [provided by RefSeq, Nov 2010]

SLX1A-SULT1A3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP7: Synonymous conserved (PhyloP=-2.31 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SULT1A3	NM_177552.4	c.105A>G	p.Gln35=	synonymous_variant	2/8	ENST00000338971.10
SLX1A-SULT1A3	NR_037608.1	n.1026A>G		non_coding_transcript_exon_variant	5/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SULT1A3	ENST00000338971.10	c.105A>G	p.Gln35=	synonymous_variant	2/8	1	NM_177552.4	P4

Frequencies

GnomAD3 genomes AF: 0.400 AC: 15664 AN: 39152 Hom.: 2688 Cov.: 6

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.0883

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.413

GnomAD3 exomes AF: 0.258 AC: 14906 AN: 57808 Hom.: 331 AF XY: 0.265 AC XY: 7625 AN XY: 28826

Gnomad AFR exome AF: 0.124

Gnomad AMR exome AF: 0.212

Gnomad ASJ exome AF: 0.303

Gnomad EAS exome AF: 0.0670

Gnomad SAS exome AF: 0.274

Gnomad FIN exome AF: 0.332

Gnomad NFE exome AF: 0.372

Gnomad OTH exome AF: 0.301

GnomAD4 exome AF: 0.360 AC: 276167 AN: 766484 Hom.: 11172 Cov.: 11 AF XY: 0.358 AC XY: 137742 AN XY: 384674

Gnomad4 AFR exome AF: 0.161

Gnomad4 AMR exome AF: 0.233

Gnomad4 ASJ exome AF: 0.306

Gnomad4 EAS exome AF: 0.104

Gnomad4 SAS exome AF: 0.283

Gnomad4 FIN exome AF: 0.318

Gnomad4 NFE exome AF: 0.391

Gnomad4 OTH exome AF: 0.339

GnomAD4 genome AF: 0.400 AC: 15655 AN: 39168 Hom.: 2685 Cov.: 6 AF XY: 0.395 AC XY: 7001 AN XY: 17736

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.0877

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.404

Alfa AF: 0.363 Hom.: 878

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.35
Dann	Benign	0.39

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

Publications

LitVar

Other links and lift over

dbSNP: rs1975350; hg19: chr16-30212154; COSMIC: COSV52148126; COSMIC: COSV52148126;