2-37185792-T-G

Variant names:

• chr2-37185792-T-G
• rs11895771
• NM_001367551.1:c.312+1563A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367551.1(SULT6B1):​c.312+1563A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 150,246 control chromosomes in the GnomAD database, including 6,682 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 0.27 (6682 hom., cov: 28)
• Consequence: SULT6B1 NM_001367551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.729

Genes affected

SULT6B1 (HGNC:33433): (sulfotransferase family 6B member 1) Predicted to enable sulfotransferase activity. Predicted to be involved in sulfation. Predicted to be located in cytosol. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT6B1	NM_001367551.1	c.312+1563A>C		intron_variant	Intron 2 of 6	ENST00000535679.6	NP_001354480.1
SULT6B1	NM_001032377.2	c.198+1563A>C		intron_variant	Intron 4 of 8		NP_001027549.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT6B1	ENST00000535679.6	c.312+1563A>C		intron_variant	Intron 2 of 6	1	NM_001367551.1	ENSP00000444081.1
SULT6B1	ENST00000407963.2	c.198+1563A>C		intron_variant	Intron 3 of 7	5		ENSP00000384950.1
SULT6B1	ENST00000689208.1	n.*82+1563A>C		intron_variant	Intron 2 of 6			ENSP00000510164.1
SULT6B1	ENST00000692190.1	n.198+1563A>C		intron_variant	Intron 2 of 6			ENSP00000509090.1

Frequencies

GnomAD3 genomes AF: 0.272 AC: 40909 AN: 150160 Hom.: 6674 Cov.: 28

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.268

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.272 AC: 40929 AN: 150246 Hom.: 6682 Cov.: 28 AF XY: 0.275 AC XY: 20172 AN XY: 73270

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.275

Alfa AF: 0.274 Hom.: 1039

Bravo AF: 0.290

Asia WGS AF: 0.585 AC: 2034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.0
DANN	Benign	0.44

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: rs11895771; hg19: chr2-37412935;