1-210362834-C-CT

Variant names:

• chr1-210362834-C-CT
• rs371568839
• NM_018194.6:c.92-7dupT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_018194.6(HHAT):​c.92-7dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.025 in 1,070,256 control chromosomes in the GnomAD database, including 8 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0063 (7 hom., cov: 32)
  • Exomes 𝑓: 0.028 (1 hom.)
• Consequence: HHAT NM_018194.6 splice_region, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.250

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]

ENSG00000287354 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-210362834-C-CT is Benign according to our data. Variant chr1-210362834-C-CT is described in ClinVar as [Benign]. Clinvar id is 1601509.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HHAT	NM_018194.6	c.92-7dupT		splice_region_variant, intron_variant	Intron 2 of 11	ENST00000261458.8	NP_060664.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HHAT	ENST00000261458.8	c.92-18_92-17insT		intron_variant	Intron 2 of 11	2	NM_018194.6	ENSP00000261458.3

Frequencies

GnomAD3 genomes AF: 0.00626 AC: 918 AN: 146628 Hom.: 7 Cov.: 32

Gnomad AFR AF: 0.0193

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00378

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000792

Gnomad SAS AF: 0.000432

Gnomad FIN AF: 0.000213

Gnomad MID AF: 0.00649

Gnomad NFE AF: 0.00106

Gnomad OTH AF: 0.00450

GnomAD4 exome AF: 0.0280 AC: 25879 AN: 923562 Hom.: 1 Cov.: 24 AF XY: 0.0271 AC XY: 12428 AN XY: 459408

Gnomad4 AFR exome AF: 0.0550

Gnomad4 AMR exome AF: 0.0302

Gnomad4 ASJ exome AF: 0.0234

Gnomad4 EAS exome AF: 0.0186

Gnomad4 SAS exome AF: 0.0265

Gnomad4 FIN exome AF: 0.0188

Gnomad4 NFE exome AF: 0.0282

Gnomad4 OTH exome AF: 0.0273

GnomAD4 genome AF: 0.00625 AC: 917 AN: 146694 Hom.: 7 Cov.: 32 AF XY: 0.00608 AC XY: 434 AN XY: 71338

Gnomad4 AFR AF: 0.0193

Gnomad4 AMR AF: 0.00370

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000596

Gnomad4 SAS AF: 0.000433

Gnomad4 FIN AF: 0.000213

Gnomad4 NFE AF: 0.00106

Gnomad4 OTH AF: 0.00446

Bravo AF: 0.00659

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 09, 2021

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs371568839; hg19: chr1-210536178;