rs992038

Positions:

• chr4-69809118-G-A
• chr4-69809118-G-C
• chr4-69809118-G-T

Variant summary

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

The ENST00000458020.1(SULT1D1P):​n.369+712C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.952 in 152,226 control chromosomes in the GnomAD database, including 69,189 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 0.95 (69189 hom., cov: 32)
• Consequence: SULT1D1P ENST00000458020.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

Genes affected

SULT1D1P (HGNC:30659): (sulfotransferase family 1D member 1, pseudogene) Sulfotransferase enzymes catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs, and xenobiotic compounds. This gene has been inactivated by mutation and is nonfunctional in humans. [provided by RefSeq, Oct 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.986 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SULT1D1P	ENST00000458020.1	n.369+712C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.952 AC: 144847 AN: 152108 Hom.: 69142 Cov.: 32

Gnomad AFR AF: 0.883

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.992

Gnomad EAS AF: 0.914

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.980

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.993

Gnomad OTH AF: 0.955

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

GnomAD4 genome AF: 0.952 AC: 144953 AN: 152226 Hom.: 69189 Cov.: 32 AF XY: 0.950 AC XY: 70745 AN XY: 74436

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.936

Gnomad4 ASJ AF: 0.992

Gnomad4 EAS AF: 0.914

Gnomad4 SAS AF: 0.970

Gnomad4 FIN AF: 0.980

Gnomad4 NFE AF: 0.993

Gnomad4 OTH AF: 0.954

Alfa AF: 0.978 Hom.: 30002

Bravo AF: 0.946

Asia WGS AF: 0.944 AC: 3284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs992038; hg19: chr4-70674836;