rs7678936

Variant names:

• chr4-99157733-A-C
• rs7678936
• ENST00000500358.6:n.3714+154A>C

Your query was ambiguous. Multiple possible variants found:

• chr4-99157733-A-C
• chr4-99157733-A-T

Variant summary

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

The ENST00000504581.1(ADH4):​n.60T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 152,172 control chromosomes in the GnomAD database, including 60,656 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 0.89 (60656 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ADH4 ENST00000504581.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.866

Genes affected

ENSG00000246090 (HGNC:):

ADH4 (HGNC:252): (alcohol dehydrogenase 4 (class II), pi polypeptide) This gene encodes class II alcohol dehydrogenase 4 pi 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 II alcohol dehydrogenase is a homodimer composed of 2 pi subunits. It exhibits a high activity for oxidation of long-chain aliphatic alcohols and aromatic alcohols and is less sensitive to pyrazole. This gene is localized to chromosome 4 in the cluster of alcohol dehydrogenase genes. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.3714+154A>C		intron_variant	Intron 3 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.3714+154A>C		intron_variant	Intron 3 of 9	1
ADH4	ENST00000504581.1	n.60T>G		non_coding_transcript_exon_variant	Exon 1 of 3	3
ENSG00000246090	ENST00000661393.1	n.765+154A>C		intron_variant	Intron 3 of 9
ENSG00000246090	ENST00000691990.1	n.535+154A>C		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135130 AN: 152054 Hom.: 60629 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.978

Gnomad AMR AF: 0.926

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.916

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.889 AC: 135206 AN: 152172 Hom.: 60656 Cov.: 32 AF XY: 0.890 AC XY: 66236 AN XY: 74422

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.926

Gnomad4 ASJ AF: 0.963

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.968

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.917

Alfa AF: 0.938 Hom.: 133276

Bravo AF: 0.881

Asia WGS AF: 0.961 AC: 3342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.70
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7678936; hg19: chr4-100078890;