NM_001055.4:c.-5+452G>A

Variant names:

• chr16-28609479-C-T
• rs3760091
• NM_001055.4:c.-5+452G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001055.4(SULT1A1):​c.-5+452G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 37)
• Consequence: SULT1A1 NM_001055.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 29 publications found

Genes affected

SULT1A1 (HGNC:11453): (sulfotransferase family 1A member 1) 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 one of two phenol sulfotransferases with thermostable enzyme activity. Multiple alternatively spliced variants that encode two isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

ENSG00000289755 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001055.4. 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
	SULT1A1	NM_001055.4	MANE Select	c.-5+452G>A		intron	N/A	NP_001046.2
	SULT1A1	NM_001394422.1		c.-425G>A		5_prime_UTR_premature_start_codon_gain	Exon 3 of 10	NP_001381351.1	P50225-1
	SULT1A1	NM_177530.4		c.-425G>A		5_prime_UTR_premature_start_codon_gain	Exon 1 of 8	NP_803566.1	P50225-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULT1A1	ENST00000314752.12	TSL:1 MANE Select	c.-5+452G>A		intron	N/A	ENSP00000321988.7	P50225-1
	ENSG00000289755	ENST00000562058.5	TSL:1	n.755+452G>A		intron	N/A
	ENSG00000289755	ENST00000564818.5	TSL:1	n.455-44G>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 37

GnomAD4 exome Cov.: 15

GnomAD4 genome Cov.: 37

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.069
DANN	Benign	0.16
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs3760091; hg19: chr16-28620800;