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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;