1-165697211-C-T

Position:

• chr1-165697211-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALDH9A1	NM_000696.4	c.181+1167G>A		intron_variant		ENST00000354775.5	NP_000687.3
ALDH9A1	NM_001365774.2	c.-102+1039G>A		intron_variant			NP_001352703.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALDH9A1	ENST00000354775.5	c.181+1167G>A		intron_variant		1	NM_000696.4	ENSP00000346827	P1
ALDH9A1	ENST00000461664.5	n.291+1039G>A		intron_variant, non_coding_transcript_variant		3
ALDH9A1	ENST00000471457.1	n.136+1167G>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.635

Alfa AF: 0.623 Hom.: 27298

Bravo AF: 0.619

Asia WGS AF: 0.574 AC: 1994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.40

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: rs10753688; hg19: chr1-165666448;