6-31018261-G-C

Variant names:

• chr6-31018261-G-C
• rs2894176
• NM_001395414.1:c.71-7241G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000561890.1(MUC22):​c.71-7241G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,952 control chromosomes in the GnomAD database, including 15,316 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 0.45 (15316 hom., cov: 32)
• Consequence: MUC22 ENST00000561890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636
• Publications: 9 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000561890.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUC22	NM_001395414.1	MANE Select	c.71-7241G>C		intron	N/A	NP_001382343.1
	MUC22	NM_001318484.1		c.80-7241G>C		intron	N/A	NP_001305413.1
	MUC22	NM_001198815.1		c.71-7241G>C		intron	N/A	NP_001185744.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUC22	ENST00000561890.1	TSL:2 MANE Select	c.71-7241G>C		intron	N/A	ENSP00000455906.1

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67705 AN: 151834 Hom.: 15300 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.446 AC: 67753 AN: 151952 Hom.: 15316 Cov.: 32 AF XY: 0.450 AC XY: 33400 AN XY: 74266

African (AFR) AF: 0.482 AC: 19962 AN: 41404

American (AMR) AF: 0.415 AC: 6351 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1640 AN: 3468

East Asian (EAS) AF: 0.543 AC: 2804 AN: 5162

South Asian (SAS) AF: 0.467 AC: 2254 AN: 4830

European-Finnish (FIN) AF: 0.461 AC: 4856 AN: 10524

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28265 AN: 67960

Other (OTH) AF: 0.451 AC: 949 AN: 2102

Alfa AF: 0.252 Hom.: 562

Bravo AF: 0.443

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.51
PhyloP100		-0.64
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2894176; hg19: chr6-30986038;