chr2-37185792-T-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367551.1. 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
	SULT6B1	NM_001367551.1	MANE Select	c.312+1563A>C		intron	N/A	NP_001354480.1
	SULT6B1	NM_001032377.2		c.198+1563A>C		intron	N/A	NP_001027549.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULT6B1	ENST00000535679.6	TSL:1 MANE Select	c.312+1563A>C		intron	N/A	ENSP00000444081.1
	SULT6B1	ENST00000407963.2	TSL:5	c.198+1563A>C		intron	N/A	ENSP00000384950.1
	SULT6B1	ENST00000689208.1		n.*82+1563A>C		intron	N/A	ENSP00000510164.1

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

African (AFR) AF: 0.246 AC: 10018 AN: 40778

American (AMR) AF: 0.393 AC: 5915 AN: 15048

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 654 AN: 3454

East Asian (EAS) AF: 0.787 AC: 4026 AN: 5118

South Asian (SAS) AF: 0.406 AC: 1926 AN: 4746

European-Finnish (FIN) AF: 0.194 AC: 1979 AN: 10198

Middle Eastern (MID) AF: 0.236 AC: 67 AN: 284

European-Non Finnish (NFE) AF: 0.229 AC: 15459 AN: 67634

Other (OTH) AF: 0.275 AC: 572 AN: 2082

Alfa AF: 0.273 Hom.: 1065

Bravo AF: 0.290

Asia WGS AF: 0.585 AC: 2034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.0
DANN	Benign	0.44
PhyloP100		0.73
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: rs11895771; hg19: chr2-37412935;