Genetic Variant MUC22:c.71-7264A>G (chr6-31018238-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001395414.1(MUC22):c.71-7264A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 152,014 control chromosomes in the GnomAD database, including 11,485 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 0.39 ( 11485 hom., cov: 33)

Consequence

MUC22
NM_001395414.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00300

Variant links:

Genes affected

MUC22 (HGNC:39755): (mucin 22) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

MUC22 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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
MUC22	NM_001395414.1 link	c.71-7264A>G	intron_variant	Intron 1 of 3	ENST00000561890.1	NP_001382343.1
MUC22	NM_001318484.1 link	c.80-7264A>G	intron_variant	Intron 2 of 4		NP_001305413.1	E2RYF6
MUC22	NM_001198815.1 link	c.71-7264A>G	intron_variant	Intron 2 of 4		NP_001185744.1	E2RYF6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC22	ENST00000561890.1 link	c.71-7264A>G		intron_variant	Intron 1 of 3	2	NM_001395414.1	ENSP00000455906.1		E2RYF6

Frequencies

GnomAD3 genomes

AF:

0.385

AC:

58512

AN:

151896

Hom.:

11472

Cov.:

show subpopulations

Gnomad AFR

AF:

0.429

Gnomad AMI

AF:

0.480

Gnomad AMR

AF:

0.336

Gnomad ASJ

AF:

0.439

Gnomad EAS

AF:

0.470

Gnomad SAS

AF:

0.349

Gnomad FIN

AF:

0.427

Gnomad MID

AF:

0.386

Gnomad NFE

AF:

0.355

Gnomad OTH

AF:

0.380

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

GnomAD4 genome

AF:

0.385

AC:

58550

AN:

152014

Hom.:

11485

Cov.:

AF XY:

0.389

AC XY:

28933

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.429

Gnomad4 AMR

AF:

0.336

Gnomad4 ASJ

AF:

0.439

Gnomad4 EAS

AF:

0.469

Gnomad4 SAS

AF:

0.349

Gnomad4 FIN

AF:

0.427

Gnomad4 NFE

AF:

0.355

Gnomad4 OTH

AF:

0.379

Alfa

AF:

0.353

Hom.:

2811

Bravo

AF:

0.381

Asia WGS

AF:

0.369

AC:

1282

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

5.3

DANN

Benign

0.76

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