rs854151

chr15-50250522-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002112.4(HDC):c.1041+1908T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,014 control chromosomes in the GnomAD database, including 4,578 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 0.24 (4578 hom., cov: 32)
• Consequence: HDC NM_002112.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326

Genes affected

HDC (HGNC:4855): (histidine decarboxylase) This gene encodes a member of the group II decarboxylase family and forms a homodimer that converts L-histidine to histamine in a pyridoxal phosphate dependent manner. Histamine regulates several physiologic processes, including neurotransmission, gastric acid secretion,inflamation, and smooth muscle tone.[provided by RefSeq, Aug 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HDC	NM_002112.4	c.1041+1908T>C		intron_variant		ENST00000267845.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HDC	ENST00000267845.8	c.1041+1908T>C		intron_variant		1	NM_002112.4	P1
HDC	ENST00000543581.5	c.1041+1908T>C		intron_variant		1
HDC	ENST00000559816.1	n.785+1908T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36958 AN: 151896 Hom.: 4576 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.243 AC: 36989 AN: 152014 Hom.: 4578 Cov.: 32 AF XY: 0.247 AC XY: 18337 AN XY: 74278

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.256

Alfa AF: 0.250 Hom.: 6501

Bravo AF: 0.232

Asia WGS AF: 0.271 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.31
Dann	Benign	0.61

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: rs854151; hg19: chr15-50542719;