rs6659502

Variant names:

• chr1-210672986-G-A
• rs6659502
• NM_018194.6:c.1391-1302G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-210672986-G-A
• chr1-210672986-G-C
• chr1-210672986-G-T

Variant summary

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

The NM_018194.6(HHAT):​c.1391-1302G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 152,142 control chromosomes in the GnomAD database, including 42,779 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 0.73 (42779 hom., cov: 32)
• Consequence: HHAT NM_018194.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 1 publications found

Genes affected

HHAT (HGNC:18270): (hedgehog acyltransferase) 'Skinny hedgehog' (SKI1) encodes an enzyme that acts within the secretory pathway to catalyze amino-terminal palmitoylation of 'hedgehog' (see MIM 600725).[supplied by OMIM, Jul 2002]

HHAT Gene-Disease associations (from GenCC):

• chondrodysplasia-pseudohermaphroditism syndrome

  Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, PanelApp Australia, Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HHAT	NM_018194.6	c.1391-1302G>A		intron_variant	Intron 11 of 11	ENST00000261458.8	NP_060664.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HHAT	ENST00000261458.8	c.1391-1302G>A		intron_variant	Intron 11 of 11	2	NM_018194.6	ENSP00000261458.3

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110495 AN: 152022 Hom.: 42775 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.821

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.726 AC: 110527 AN: 152142 Hom.: 42779 Cov.: 32 AF XY: 0.728 AC XY: 54154 AN XY: 74386

African (AFR) AF: 0.449 AC: 18618 AN: 41448

American (AMR) AF: 0.750 AC: 11478 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3036 AN: 3470

East Asian (EAS) AF: 0.509 AC: 2625 AN: 5156

South Asian (SAS) AF: 0.831 AC: 4005 AN: 4822

European-Finnish (FIN) AF: 0.851 AC: 9024 AN: 10608

Middle Eastern (MID) AF: 0.825 AC: 241 AN: 292

European-Non Finnish (NFE) AF: 0.870 AC: 59159 AN: 68026

Other (OTH) AF: 0.766 AC: 1617 AN: 2112

Alfa AF: 0.791 Hom.: 32730

Bravo AF: 0.701

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.6
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs6659502; hg19: chr1-210846327;