rs28360974

Positions:

• chr6-31008442-G-A

Variant summary

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

The NM_001318484.1(MUC22):​c.8-2263G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0341 in 152,270 control chromosomes in the GnomAD database, including 106 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 0.034 (106 hom., cov: 32)
• Consequence: MUC22 NM_001318484.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119

Genes affected

MUC22 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUC22	NM_001198815.1	c.-37-2228G>A		intron_variant			NP_001185744.1
MUC22	NM_001318484.1	c.8-2263G>A		intron_variant			NP_001305413.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0341 AC: 5190 AN: 152152 Hom.: 107 Cov.: 32

Gnomad AFR AF: 0.0315

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.0342

Gnomad ASJ AF: 0.0257

Gnomad EAS AF: 0.00481

Gnomad SAS AF: 0.0661

Gnomad FIN AF: 0.0155

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0380

Gnomad OTH AF: 0.0397

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

GnomAD4 genome AF: 0.0341 AC: 5197 AN: 152270 Hom.: 106 Cov.: 32 AF XY: 0.0334 AC XY: 2489 AN XY: 74456

Gnomad4 AFR AF: 0.0315

Gnomad4 AMR AF: 0.0342

Gnomad4 ASJ AF: 0.0257

Gnomad4 EAS AF: 0.00482

Gnomad4 SAS AF: 0.0674

Gnomad4 FIN AF: 0.0155

Gnomad4 NFE AF: 0.0380

Gnomad4 OTH AF: 0.0393

Alfa AF: 0.0358 Hom.: 37

Bravo AF: 0.0341

Asia WGS AF: 0.0200 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs28360974; hg19: chr6-30976219;