Variant 7-1435155-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_182924.4(MICALL2):c.2592-8C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00502 in 1,613,384 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0035 ( 1 hom., cov: 31)

Exomes 𝑓: 0.0052 ( 24 hom. )

Consequence

MICALL2
NM_182924.4 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.00004014

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.391

Variant links:

Genes affected

MICALL2 (HGNC:29672): (MICAL like 2) Enables filamin binding activity. Involved in positive regulation of protein targeting to mitochondrion. Predicted to be located in several cellular components, including bicellular tight junction; neuron projection; and recycling endosome. Predicted to colocalize with stress fiber. [provided by Alliance of Genome Resources, Apr 2022]

MICALL2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 7-1435155-G-A is Benign according to our data. Variant chr7-1435155-G-A is described in ClinVar as [Benign]. Clinvar id is 731542.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 24 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MICALL2	NM_182924.4 linkuse as main transcript	c.2592-8C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000297508.8	NP_891554.1
MICALL2	XM_047420838.1 linkuse as main transcript	c.1359-8C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant			XP_047276794.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MICALL2	ENST00000297508.8 linkuse as main transcript	c.2592-8C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_182924.4	ENSP00000297508	P1	Q8IY33-1

Frequencies

GnomAD3 genomes

AF:

0.00352

AC:

536

AN:

152180

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00101

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00118

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00800

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00567

Gnomad OTH

AF:

0.00143

GnomAD3 exomes

AF:

0.00342

AC:

855

AN:

250272

Hom.:

AF XY:

0.00343

AC XY:

465

AN XY:

135664

show subpopulations

Gnomad AFR exome

AF:

0.00155

Gnomad AMR exome

AF:

0.00122

Gnomad ASJ exome

AF:

0.000499

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000261

Gnomad FIN exome

AF:

0.00668

Gnomad NFE exome

AF:

0.00543

Gnomad OTH exome

AF:

0.00294

GnomAD4 exome

AF:

0.00518

AC:

7566

AN:

1461086

Hom.:

Cov.:

AF XY:

0.00496

AC XY:

3604

AN XY:

726842

show subpopulations

Gnomad4 AFR exome

AF:

0.00125

Gnomad4 AMR exome

AF:

0.00116

Gnomad4 ASJ exome

AF:

0.000498

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000209

Gnomad4 FIN exome

AF:

0.00595

Gnomad4 NFE exome

AF:

0.00616

Gnomad4 OTH exome

AF:

0.00450

GnomAD4 genome

AF:

0.00352

AC:

536

AN:

152298

Hom.:

Cov.:

AF XY:

0.00356

AC XY:

265

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.00101

Gnomad4 AMR

AF:

0.00118

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00800

Gnomad4 NFE

AF:

0.00567

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00403

Hom.:

Bravo

AF:

0.00299

Asia WGS

AF:

0.000289

AC:

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

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.94

DANN

Benign

0.51

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000040

dbscSNV1_RF

Benign

0.0020

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