rs2000864

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_037884.1(LOC100507053):​n.3715-1738C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 396,300 control chromosomes in the GnomAD database, including 63,587 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 0.56 ( 24730 hom., cov: 32)
Exomes 𝑓: 0.55 ( 38857 hom. )

Consequence

LOC100507053
NR_037884.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.398
Variant links:
Genes affected
ADH6 (HGNC:255): (alcohol dehydrogenase 6 (class V)) This gene encodes class V alcohol dehydrogenase, which is a member of the alcohol dehydrogenase family. Members of this family metabolize a wide variety of substrates, including ethanol, retinol, other aliphatic alcohols, hydroxysteroids, and lipid peroxidation products. This gene is expressed in the stomach as well as in the liver, and it contains a glucocorticoid response element upstream of its 5' UTR, which is a steroid hormone receptor binding site. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

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 = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC100507053NR_037884.1 linkuse as main transcriptn.3715-1738C>A intron_variant, non_coding_transcript_variant
ADH6NM_001102470.2 linkuse as main transcript downstream_gene_variant ENST00000394899.6 NP_001095940.1
ADH6NM_000672.4 linkuse as main transcript downstream_gene_variant NP_000663.1
ADH6NR_132990.2 linkuse as main transcript downstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000500358.6 linkuse as main transcriptn.3715-1738C>A intron_variant, non_coding_transcript_variant 1
ADH6ENST00000394899.6 linkuse as main transcript downstream_gene_variant 2 NM_001102470.2 ENSP00000378359 P1P28332-2

Frequencies

GnomAD3 genomes
AF:
0.563
AC:
85451
AN:
151868
Hom.:
24707
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.642
Gnomad AMI
AF:
0.582
Gnomad AMR
AF:
0.599
Gnomad ASJ
AF:
0.571
Gnomad EAS
AF:
0.879
Gnomad SAS
AF:
0.561
Gnomad FIN
AF:
0.465
Gnomad MID
AF:
0.506
Gnomad NFE
AF:
0.497
Gnomad OTH
AF:
0.568
GnomAD4 exome
AF:
0.549
AC:
134226
AN:
244316
Hom.:
38857
Cov.:
0
AF XY:
0.549
AC XY:
67969
AN XY:
123882
show subpopulations
Gnomad4 AFR exome
AF:
0.650
Gnomad4 AMR exome
AF:
0.587
Gnomad4 ASJ exome
AF:
0.574
Gnomad4 EAS exome
AF:
0.895
Gnomad4 SAS exome
AF:
0.535
Gnomad4 FIN exome
AF:
0.468
Gnomad4 NFE exome
AF:
0.503
Gnomad4 OTH exome
AF:
0.548
GnomAD4 genome
AF:
0.563
AC:
85521
AN:
151984
Hom.:
24730
Cov.:
32
AF XY:
0.562
AC XY:
41785
AN XY:
74286
show subpopulations
Gnomad4 AFR
AF:
0.642
Gnomad4 AMR
AF:
0.599
Gnomad4 ASJ
AF:
0.571
Gnomad4 EAS
AF:
0.879
Gnomad4 SAS
AF:
0.560
Gnomad4 FIN
AF:
0.465
Gnomad4 NFE
AF:
0.497
Gnomad4 OTH
AF:
0.566
Alfa
AF:
0.516
Hom.:
32423
Bravo
AF:
0.578
Asia WGS
AF:
0.629
AC:
2187
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
0.67
DANN
Benign
0.70

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2000864; hg19: chr4-100123776; API