rs6423191

Variant names:

• chr1-21431376-G-A
• rs6423191

Your query was ambiguous. Multiple possible variants found:

• chr1-21431376-G-A
• chr1-21431376-G-C

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 0.558 in 151,798 control chromosomes in the GnomAD database, including 25,706 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 0.56 (25706 hom., cov: 31)
• Consequence: HS6ST1P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420
• Publications: 3 publications found

Genes affected

HS6ST1P1 (HGNC:31835): (heparan sulfate 6-O-sulfotransferase 1 pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HS6ST1P1		n.21431376G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84677 AN: 151680 Hom.: 25718 Cov.: 31

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.558 AC: 84678 AN: 151798 Hom.: 25706 Cov.: 31 AF XY: 0.558 AC XY: 41353 AN XY: 74160

African (AFR) AF: 0.310 AC: 12839 AN: 41464

American (AMR) AF: 0.615 AC: 9383 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2303 AN: 3466

East Asian (EAS) AF: 0.768 AC: 3937 AN: 5128

South Asian (SAS) AF: 0.542 AC: 2612 AN: 4818

European-Finnish (FIN) AF: 0.643 AC: 6781 AN: 10540

Middle Eastern (MID) AF: 0.709 AC: 207 AN: 292

European-Non Finnish (NFE) AF: 0.659 AC: 44720 AN: 67816

Other (OTH) AF: 0.590 AC: 1244 AN: 2110

Alfa AF: 0.597 Hom.: 6614

Bravo AF: 0.548

Asia WGS AF: 0.604 AC: 2097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.2
DANN	Benign	0.46
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs6423191; hg19: chr1-21757869;