Variant 12-85280680-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_006982.3(ALX1):c.226+193C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 151,968 control chromosomes in the GnomAD database, including 3,183 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.14 ( 3183 hom., cov: 32)

Consequence

ALX1
NM_006982.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.249

Variant links:

Genes affected

ALX1 (HGNC:1494): (ALX homeobox 1) The specific function of this gene has yet to be determined in humans; however, in rodents, it is necessary for survival of the forebrain mesenchyme and may also be involved in development of the cervix. Mutations in the mouse gene lead to neural tube defects such as acrania and meroanencephaly. [provided by RefSeq, Jul 2008]

ALX1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 12-85280680-C-A is Benign according to our data. Variant chr12-85280680-C-A is described in ClinVar as [Benign]. Clinvar id is 1226313.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALX1	NM_006982.3 link	c.226+193C>A		intron_variant		ENST00000316824.4	NP_008913.2	Q15699V9HWA7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALX1	ENST00000316824.4 link	c.226+193C>A		intron_variant		1	NM_006982.3	ENSP00000315417.3		Q15699

Frequencies

GnomAD3 genomes

AF:

0.144

AC:

21885

AN:

151850

Hom.:

3171

Cov.:

show subpopulations

Gnomad AFR

AF:

0.374

Gnomad AMI

AF:

0.0866

Gnomad AMR

AF:

0.0703

Gnomad ASJ

AF:

0.0487

Gnomad EAS

AF:

0.183

Gnomad SAS

AF:

0.0676

Gnomad FIN

AF:

0.0304

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0483

Gnomad OTH

AF:

0.119

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

GnomAD4 genome

AF:

0.144

AC:

21937

AN:

151968

Hom.:

3183

Cov.:

AF XY:

0.141

AC XY:

10499

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.374

Gnomad4 AMR

AF:

0.0701

Gnomad4 ASJ

AF:

0.0487

Gnomad4 EAS

AF:

0.183

Gnomad4 SAS

AF:

0.0676

Gnomad4 FIN

AF:

0.0304

Gnomad4 NFE

AF:

0.0483

Gnomad4 OTH

AF:

0.121

Alfa

AF:

0.0209

Hom.:

Bravo

AF:

0.159

Asia WGS

AF:

0.165

AC:

575

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.1

DANN

Benign

0.49

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over