rs3871466

chr6-31015906-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.70+5130T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,218 control chromosomes in the GnomAD database, including 1,323 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 0.12 (1323 hom., cov: 32)
• Consequence: MUC22 NM_001395414.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.585

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=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MUC22	NM_001395414.1	c.70+5130T>C		intron_variant		ENST00000561890.1
MUC22	NM_001198815.1	c.70+5130T>C		intron_variant
MUC22	NM_001318484.1	c.79+5130T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MUC22	ENST00000561890.1	c.70+5130T>C		intron_variant		2	NM_001395414.1	P1

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18347 AN: 152100 Hom.: 1325 Cov.: 32

Gnomad AFR AF: 0.0760

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.0920

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.120 AC: 18336 AN: 152218 Hom.: 1323 Cov.: 32 AF XY: 0.123 AC XY: 9186 AN XY: 74436

Gnomad4 AFR AF: 0.0758

Gnomad4 AMR AF: 0.0916

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.107

Alfa AF: 0.130 Hom.: 2402

Bravo AF: 0.114

Asia WGS AF: 0.216 AC: 751 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	13
Dann	Benign	0.90

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: rs3871466; hg19: chr6-30983683; COSMIC: COSV73736453;