rs9394031

Positions:

• chr6-31023866-T-C

Variant summary

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

The NM_001395414.1(MUC22):​c.71-1636T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,130 control chromosomes in the GnomAD database, including 1,213 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 0.11 (1213 hom., cov: 32)
• Consequence: MUC22 NM_001395414.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.616

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUC22	NM_001395414.1	c.71-1636T>C		intron_variant		ENST00000561890.1	NP_001382343.1
MUC22	NM_001318484.1	c.80-1636T>C		intron_variant			NP_001305413.1
MUC22	NM_001198815.1	c.71-1636T>C		intron_variant			NP_001185744.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MUC22	ENST00000561890.1	c.71-1636T>C		intron_variant		2	NM_001395414.1	ENSP00000455906.1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16766 AN: 152012 Hom.: 1215 Cov.: 32

Gnomad AFR AF: 0.0492

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.0825

Gnomad ASJ AF: 0.0882

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.0939

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

GnomAD4 genome AF: 0.110 AC: 16752 AN: 152130 Hom.: 1213 Cov.: 32 AF XY: 0.113 AC XY: 8400 AN XY: 74364

Gnomad4 AFR AF: 0.0490

Gnomad4 AMR AF: 0.0822

Gnomad4 ASJ AF: 0.0882

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.0953

Alfa AF: 0.111 Hom.: 329

Bravo AF: 0.102

Asia WGS AF: 0.214 AC: 742 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.6
DANN	Benign	0.46

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: rs9394031; hg19: chr6-30991643;