Genetic Variant MICF:n.29852501A>G (chr6-29852501-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The variant allele was found at a frequency of 0.308 in 152,216 control chromosomes in the GnomAD database, including 7,307 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 0.31 ( 7296 hom., cov: 32)

Exomes 𝑓: 0.33 ( 11 hom. )

Consequence

MICF
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.991

Variant links:

Genes affected

MICF (HGNC:16801): (MHC class I polypeptide-related sequence F (pseudogene))

MICF links:

ENSG00000290870 (HGNC:):

ENSG00000290870 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MICF		n.29852501A>G	intragenic_variant
LOC105375010	XR_926680.3 link	n.42-15T>C	intron_variant	Intron 1 of 2
LOC105375010	XR_926681.2 link	n.42-15T>C	intron_variant	Intron 1 of 3
LOC105375010	XR_926682.3 link	n.42-15T>C	intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290870	ENST00000647952.1 link	n.2156-15T>C		intron_variant	Intron 2 of 3
ENSG00000285799	ENST00000432679.1 link	n.-10T>C		upstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.308

AC:

46763

AN:

151842

Hom.:

7283

Cov.:

show subpopulations

Gnomad AFR

AF:

0.281

Gnomad AMI

AF:

0.381

Gnomad AMR

AF:

0.295

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.362

Gnomad SAS

AF:

0.167

Gnomad FIN

AF:

0.345

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.332

Gnomad OTH

AF:

0.297

GnomAD4 exome

AF:

0.332

AC:

AN:

256

Hom.:

Cov.:

AF XY:

0.307

AC XY:

AN XY:

140

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.500

Gnomad4 SAS exome

AF:

0.300

Gnomad4 FIN exome

AF:

0.315

Gnomad4 NFE exome

AF:

0.333

Gnomad4 OTH exome

AF:

0.400

GnomAD4 genome

AF:

0.308

AC:

46792

AN:

151960

Hom.:

7296

Cov.:

AF XY:

0.305

AC XY:

22648

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.281

Gnomad4 AMR

AF:

0.294

Gnomad4 ASJ

AF:

0.217

Gnomad4 EAS

AF:

0.363

Gnomad4 SAS

AF:

0.166

Gnomad4 FIN

AF:

0.345

Gnomad4 NFE

AF:

0.332

Gnomad4 OTH

AF:

0.293

Alfa

AF:

0.325

Hom.:

5524

Bravo

AF:

0.308

Asia WGS

AF:

0.218

AC:

757

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

4.3

DANN

Benign

0.35

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