Variant 3-46689259-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000318962.9(ALS2CL):c.103+79T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 1,429,354 control chromosomes in the GnomAD database, including 86,368 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 0.43 ( 15771 hom., cov: 33)

Exomes 𝑓: 0.32 ( 70597 hom. )

Consequence

ALS2CL
ENST00000318962.9 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.627

Variant links:

Genes affected

ALS2CL (HGNC:20605): (ALS2 C-terminal like) Enables identical protein binding activity. Acts upstream of or within endosome organization. Predicted to be located in cytoplasmic vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ALS2CL links:

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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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
ALS2CL	NM_147129.5 linkuse as main transcript	c.103+79T>C	intron_variant	ENST00000318962.9	NP_667340.2
ALS2CL	NM_001190707.2 linkuse as main transcript	c.103+79T>C	intron_variant		NP_001177636.1
ALS2CL	NR_033815.3 linkuse as main transcript	n.165+79T>C	intron_variant, non_coding_transcript_variant
ALS2CL	NR_135622.2 linkuse as main transcript	n.165+79T>C	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALS2CL	ENST00000318962.9 linkuse as main transcript	c.103+79T>C		intron_variant		1	NM_147129.5	ENSP00000313670	P1	Q60I27-1

Frequencies

GnomAD3 genomes

AF:

0.425

AC:

64621

AN:

151932

Hom.:

15746

Cov.:

show subpopulations

Gnomad AFR

AF:

0.681

Gnomad AMI

AF:

0.346

Gnomad AMR

AF:

0.387

Gnomad ASJ

AF:

0.347

Gnomad EAS

AF:

0.288

Gnomad SAS

AF:

0.384

Gnomad FIN

AF:

0.336

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.311

Gnomad OTH

AF:

0.421

GnomAD4 exome

AF:

0.324

AC:

414482

AN:

1277304

Hom.:

70597

AF XY:

0.326

AC XY:

207959

AN XY:

638702

show subpopulations

Gnomad4 AFR exome

AF:

0.697

Gnomad4 AMR exome

AF:

0.402

Gnomad4 ASJ exome

AF:

0.336

Gnomad4 EAS exome

AF:

0.283

Gnomad4 SAS exome

AF:

0.380

Gnomad4 FIN exome

AF:

0.328

Gnomad4 NFE exome

AF:

0.305

Gnomad4 OTH exome

AF:

0.349

GnomAD4 genome

AF:

0.425

AC:

64694

AN:

152050

Hom.:

15771

Cov.:

AF XY:

0.424

AC XY:

31510

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.681

Gnomad4 AMR

AF:

0.387

Gnomad4 ASJ

AF:

0.347

Gnomad4 EAS

AF:

0.288

Gnomad4 SAS

AF:

0.383

Gnomad4 FIN

AF:

0.336

Gnomad4 NFE

AF:

0.311

Gnomad4 OTH

AF:

0.417

Alfa

AF:

0.344

Hom.:

4941

Bravo

AF:

0.444

Asia WGS

AF:

0.336

AC:

1171

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.0

DANN

Benign

0.71

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over