Variant 12-109356932-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 NM_001101421.4(MYO1H):c.12+8960A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 152,006 control chromosomes in the GnomAD database, including 17,944 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 0.48 ( 17944 hom., cov: 31)

Consequence

MYO1H
NM_001101421.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.185

Variant links:

Genes affected

MYO1H (HGNC:13879): (myosin IH) Predicted to enable actin filament binding activity and microfilament motor activity. Predicted to be involved in actin filament organization and vesicle transport along actin filament. Predicted to be part of myosin complex. Predicted to be active in several cellular components, including actin cytoskeleton; microvillus; and vesicle. [provided by Alliance of Genome Resources, Apr 2022]

MYO1H links:

LINC01486 (HGNC:51137): (long intergenic non-protein coding RNA 1486)

LINC01486 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
MYO1H	NM_001101421.4 linkuse as main transcript	c.12+8960A>G	intron_variant	ENST00000310903.10
LINC01486	NR_120462.1 linkuse as main transcript	n.363+200T>C	intron_variant, non_coding_transcript_variant
MYO1H	XM_011538223.3 linkuse as main transcript	c.-36-31751A>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO1H	ENST00000310903.10 linkuse as main transcript	c.12+8960A>G		intron_variant		5	NM_001101421.4	P1
LINC01486	ENST00000538041.1 linkuse as main transcript	n.363+200T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.478

AC:

72532

AN:

151888

Hom.:

17907

Cov.:

show subpopulations

Gnomad AFR

AF:

0.579

Gnomad AMI

AF:

0.521

Gnomad AMR

AF:

0.541

Gnomad ASJ

AF:

0.501

Gnomad EAS

AF:

0.359

Gnomad SAS

AF:

0.349

Gnomad FIN

AF:

0.327

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.441

Gnomad OTH

AF:

0.496

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

GnomAD4 genome

AF:

0.478

AC:

72613

AN:

152006

Hom.:

17944

Cov.:

AF XY:

0.471

AC XY:

34970

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.580

Gnomad4 AMR

AF:

0.541

Gnomad4 ASJ

AF:

0.501

Gnomad4 EAS

AF:

0.358

Gnomad4 SAS

AF:

0.348

Gnomad4 FIN

AF:

0.327

Gnomad4 NFE

AF:

0.441

Gnomad4 OTH

AF:

0.491

Alfa

AF:

0.458

Hom.:

2003

Bravo

AF:

0.504

Asia WGS

AF:

0.330

AC:

1148

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

3.3

DANN

Benign

0.67

Splicing

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