6-114232132-T-C

Variant names:

• chr6-114232132-T-C
• rs1474171
• NM_153612.4:c.-338-3354A>G

Variant summary

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

The NM_153612.4(HS3ST5):​c.-338-3354A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,146 control chromosomes in the GnomAD database, including 1,893 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 0.16 (1893 hom., cov: 32)
• Consequence: HS3ST5 NM_153612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.791
• Publications: 2 publications found

Genes affected

HS3ST5 (HGNC:19419): (heparan sulfate-glucosamine 3-sulfotransferase 5) HS3ST5 belongs to a group of heparan sulfate 3-O-sulfotransferases (EC 2.8.2.23) that transfer sulfate from 3-prime-phosphoadenosine 5-prime phosphosulfate (PAPS) to heparan sulfate and heparin (Mochizuki et al., 2003 [PubMed 12740361]).[supplied by OMIM, Mar 2008]

HDAC2-AS2 (HGNC:43590): (HDAC2 and HS3ST5 antisense RNA 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153612.4. 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
	HS3ST5	NM_153612.4	MANE Select	c.-338-3354A>G		intron	N/A	NP_705840.2
	HS3ST5	NM_001387039.1		c.-226-3354A>G		intron	N/A	NP_001373968.1
	HS3ST5	NM_001387040.1		c.-33+110063A>G		intron	N/A	NP_001373969.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HS3ST5	ENST00000312719.10	TSL:2 MANE Select	c.-338-3354A>G		intron	N/A	ENSP00000427888.1
	HDAC2-AS2	ENST00000519104.5	TSL:1	n.1658-3498T>C		intron	N/A
	HDAC2-AS2	ENST00000451415.5	TSL:3	n.206+1786T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23663 AN: 152028 Hom.: 1894 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.156 AC: 23664 AN: 152146 Hom.: 1893 Cov.: 32 AF XY: 0.157 AC XY: 11671 AN XY: 74392

African (AFR) AF: 0.159 AC: 6580 AN: 41502

American (AMR) AF: 0.190 AC: 2902 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 637 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1374 AN: 5176

South Asian (SAS) AF: 0.141 AC: 682 AN: 4826

European-Finnish (FIN) AF: 0.128 AC: 1353 AN: 10600

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.142 AC: 9643 AN: 67992

Other (OTH) AF: 0.153 AC: 323 AN: 2110

Alfa AF: 0.151 Hom.: 3015

Bravo AF: 0.161

Asia WGS AF: 0.219 AC: 761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.60
PhyloP100		0.79
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: rs1474171; hg19: chr6-114553296;