chr15-100885655-C-CTT

Position:

• chr15-100885655-C-CTT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_000693.4(ALDH1A3):​c.204+299_204+300dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.044 (239 hom., cov: 0)
• Consequence: ALDH1A3 NM_000693.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.176

Genes affected

ALDH1A3 (HGNC:409): (aldehyde dehydrogenase 1 family member A3) This gene encodes an aldehyde dehydrogenase enzyme that uses retinal as a substrate. Mutations in this gene have been associated with microphthalmia, isolated 8, and expression changes have also been detected in tumor cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 15-100885655-C-CTT is Benign according to our data. Variant chr15-100885655-C-CTT is described in ClinVar as [Benign]. Clinvar id is 1246087.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALDH1A3	NM_000693.4	c.204+299_204+300dup		intron_variant		ENST00000329841.10	NP_000684.2
ALDH1A3	NM_001293815.2	c.204+299_204+300dup		intron_variant			NP_001280744.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALDH1A3	ENST00000329841.10	c.204+299_204+300dup		intron_variant		1	NM_000693.4	ENSP00000332256	P1

Frequencies

GnomAD3 genomes AF: 0.0435 AC: 6015 AN: 138296 Hom.: 236 Cov.: 0

Gnomad AFR AF: 0.0958

Gnomad AMI AF: 0.00359

Gnomad AMR AF: 0.0271

Gnomad ASJ AF: 0.0606

Gnomad EAS AF: 0.00921

Gnomad SAS AF: 0.0521

Gnomad FIN AF: 0.00374

Gnomad MID AF: 0.0333

Gnomad NFE AF: 0.0224

Gnomad OTH AF: 0.0465

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

GnomAD4 genome AF: 0.0435 AC: 6022 AN: 138304 Hom.: 239 Cov.: 0 AF XY: 0.0427 AC XY: 2850 AN XY: 66702

Gnomad4 AFR AF: 0.0960

Gnomad4 AMR AF: 0.0270

Gnomad4 ASJ AF: 0.0606

Gnomad4 EAS AF: 0.00924

Gnomad4 SAS AF: 0.0514

Gnomad4 FIN AF: 0.00374

Gnomad4 NFE AF: 0.0224

Gnomad4 OTH AF: 0.0462

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4646657; hg19: chr15-101425860;