rs13191258

chr6-31010940-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001395414.1(MUC22):c.70+164C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.041 in 144,942 control chromosomes in the GnomAD database, including 173 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 0.041 (173 hom., cov: 28)
• Consequence: MUC22 NM_001395414.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MUC22	NM_001395414.1	c.70+164C>T		intron_variant		ENST00000561890.1
MUC22	NM_001198815.1	c.70+164C>T		intron_variant
MUC22	NM_001318484.1	c.79+164C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MUC22	ENST00000561890.1	c.70+164C>T		intron_variant		2	NM_001395414.1	P1

Frequencies

GnomAD3 genomes AF: 0.0411 AC: 5955 AN: 144840 Hom.: 173 Cov.: 28

Gnomad AFR AF: 0.0114

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.0233

Gnomad ASJ AF: 0.0537

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.0830

Gnomad FIN AF: 0.0450

Gnomad MID AF: 0.0594

Gnomad NFE AF: 0.0582

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0410 AC: 5949 AN: 144942 Hom.: 173 Cov.: 28 AF XY: 0.0414 AC XY: 2899 AN XY: 70074

Gnomad4 AFR AF: 0.0114

Gnomad4 AMR AF: 0.0233

Gnomad4 ASJ AF: 0.0537

Gnomad4 EAS AF: 0.0179

Gnomad4 SAS AF: 0.0822

Gnomad4 FIN AF: 0.0450

Gnomad4 NFE AF: 0.0582

Gnomad4 OTH AF: 0.0318

Alfa AF: 0.0522 Hom.: 310

Bravo AF: 0.0357

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.4
Dann	Benign	0.43

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

Other links and lift over

dbSNP: rs13191258; hg19: chr6-30978717;