rs17036146

Positions:

• chr2-108329613-G-A

Variant summary

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

The ENST00000427208.5(SULT1C5P):​n.445+97G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,992 control chromosomes in the GnomAD database, including 4,609 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 0.24 (4609 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SULT1C5P ENST00000427208.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

Genes affected

SULT1C5P (HGNC:):

SULT1C5P (HGNC:33545): (sulfotransferase family 1C member 5, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SULT1C5P	NR_037191.1	n.445+97G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SULT1C5P	ENST00000427208.5	n.445+97G>A		intron_variant		2
SULT1C5P	ENST00000562418.1	n.330+97G>A		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36244 AN: 151874 Hom.: 4600 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0587

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.238

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome AF: 0.239 AC: 36279 AN: 151992 Hom.: 4609 Cov.: 32 AF XY: 0.236 AC XY: 17520 AN XY: 74284

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.0588

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.235

Alfa AF: 0.236 Hom.: 8731

Bravo AF: 0.236

Asia WGS AF: 0.143 AC: 496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.5
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17036146; hg19: chr2-108946069;