1-165697211-C-T

Variant names:

• chr1-165697211-C-T
• rs10753688
• NM_000696.4:c.181+1167G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000696.4(ALDH9A1):​c.181+1167G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,138 control chromosomes in the GnomAD database, including 29,503 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 0.62 (29503 hom., cov: 34)
• Consequence: ALDH9A1 NM_000696.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 5 publications found

Genes affected

ALDH9A1 (HGNC:412): (aldehyde dehydrogenase 9 family member A1) This protein belongs to the aldehyde dehydrogenase family of proteins. It has a high activity for oxidation of gamma-aminobutyraldehyde and other amino aldehydes. The enzyme catalyzes the dehydrogenation of gamma-aminobutyraldehyde to gamma-aminobutyric acid (GABA). This isozyme is a tetramer of identical 54-kD subunits. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000696.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALDH9A1	NM_000696.4	MANE Select	c.181+1167G>A		intron	N/A	NP_000687.3
	ALDH9A1	NM_001365774.2		c.-102+1039G>A		intron	N/A	NP_001352703.1	P49189-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALDH9A1	ENST00000354775.5	TSL:1 MANE Select	c.181+1167G>A		intron	N/A	ENSP00000346827.4	P49189-3
	ALDH9A1	ENST00000865475.1		c.181+1167G>A		intron	N/A	ENSP00000535534.1
	ALDH9A1	ENST00000865474.1		c.151+1197G>A		intron	N/A	ENSP00000535533.1

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94465 AN: 152020 Hom.: 29465 Cov.: 34

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.622 AC: 94558 AN: 152138 Hom.: 29503 Cov.: 34 AF XY: 0.623 AC XY: 46350 AN XY: 74382

African (AFR) AF: 0.636 AC: 26408 AN: 41504

American (AMR) AF: 0.653 AC: 9978 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2483 AN: 3472

East Asian (EAS) AF: 0.394 AC: 2038 AN: 5168

South Asian (SAS) AF: 0.635 AC: 3068 AN: 4830

European-Finnish (FIN) AF: 0.622 AC: 6580 AN: 10576

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 42017 AN: 67990

Other (OTH) AF: 0.635 AC: 1343 AN: 2114

Alfa AF: 0.624 Hom.: 35658

Bravo AF: 0.619

Asia WGS AF: 0.574 AC: 1994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.40
PhyloP100		0.0020
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10753688; hg19: chr1-165666448;