chr4-99345478-A-G

Position:

• chr4-99345478-A-G

Variant summary

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

The NM_000669.5(ADH1C):​c.260-212T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,166 control chromosomes in the GnomAD database, including 8,851 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 0.31 (8851 hom., cov: 33)
• Consequence: ADH1C NM_000669.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853

Genes affected

ADH1C (HGNC:251): (alcohol dehydrogenase 1C (class I), gamma polypeptide) This gene encodes class I alcohol dehydrogenase, gamma subunit, which is a member of the alcohol dehydrogenase family. Members of this enzyme family metabolize a wide variety of substrates, including ethanol, retinol, other aliphatic alcohols, hydroxysteroids, and lipid peroxidation products. Class I alcohol dehydrogenase, consisting of several homo- and heterodimers of alpha, beta, and gamma subunits, exhibits high activity for ethanol oxidation to acetaldehyde, thus playing a major role in ethanol catabolism. Three genes encoding alpha, beta and gamma subunits are tandemly organized in a genomic segment as a gene cluster. An association between ADH1C polymorphism and alcohol dependence has not been established. [provided by RefSeq, Sep 2019]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADH1C	NM_000669.5	c.260-212T>C		intron_variant		ENST00000515683.6	NP_000660.1
ADH1C	NR_133005.2	n.331-212T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADH1C	ENST00000515683.6	c.260-212T>C		intron_variant		1	NM_000669.5	ENSP00000426083	P1
ADH1C	ENST00000510055.5	c.140-212T>C		intron_variant		3		ENSP00000478439
ADH1C	ENST00000511397.3	c.158-212T>C		intron_variant		3		ENSP00000478545
ADH1C	ENST00000505942.2	n.329-258T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47467 AN: 152048 Hom.: 8845 Cov.: 33

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0815

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.312 AC: 47488 AN: 152166 Hom.: 8851 Cov.: 33 AF XY: 0.313 AC XY: 23248 AN XY: 74374

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.0811

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.282

Alfa AF: 0.373 Hom.: 1465

Bravo AF: 0.287

Asia WGS AF: 0.220 AC: 762 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.58

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: rs1662052; hg19: chr4-100266635;