rs992038

Variant names:

• chr4-69809118-G-A
• rs992038

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

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 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SULT1D1P		n.69809118G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT1D1P	ENST00000458020.1	n.369+712C>T		intron_variant	Intron 3 of 6	6

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

African (AFR) AF: 0.883 AC: 36663 AN: 41512

American (AMR) AF: 0.936 AC: 14305 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.992 AC: 3443 AN: 3472

East Asian (EAS) AF: 0.914 AC: 4735 AN: 5180

South Asian (SAS) AF: 0.970 AC: 4679 AN: 4824

European-Finnish (FIN) AF: 0.980 AC: 10400 AN: 10610

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.993 AC: 67524 AN: 68034

Other (OTH) AF: 0.954 AC: 2012 AN: 2110

Alfa AF: 0.975 Hom.: 129369

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
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs992038; hg19: chr4-70674836;