NM_001395414.1:c.71-7264A>G

Variant names:

• chr6-31018238-A-G
• rs9262492
• NM_001395414.1:c.71-7264A>G

Variant summary

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

The NM_001395414.1(MUC22):​c.71-7264A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 152,014 control chromosomes in the GnomAD database, including 11,485 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 0.39 (11485 hom., cov: 33)
• Consequence: MUC22 NM_001395414.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 11 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395414.1. 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.71-7264A>G		intron	N/A	NP_001382343.1
	MUC22	NM_001318484.1		c.80-7264A>G		intron	N/A	NP_001305413.1
	MUC22	NM_001198815.1		c.71-7264A>G		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.71-7264A>G		intron	N/A	ENSP00000455906.1

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58512 AN: 151896 Hom.: 11472 Cov.: 33

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.385 AC: 58550 AN: 152014 Hom.: 11485 Cov.: 33 AF XY: 0.389 AC XY: 28933 AN XY: 74300

African (AFR) AF: 0.429 AC: 17777 AN: 41442

American (AMR) AF: 0.336 AC: 5134 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1522 AN: 3468

East Asian (EAS) AF: 0.469 AC: 2423 AN: 5162

South Asian (SAS) AF: 0.349 AC: 1687 AN: 4828

European-Finnish (FIN) AF: 0.427 AC: 4505 AN: 10562

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24151 AN: 67964

Other (OTH) AF: 0.379 AC: 799 AN: 2108

Alfa AF: 0.355 Hom.: 19221

Bravo AF: 0.381

Asia WGS AF: 0.369 AC: 1282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.3
DANN	Benign	0.76
PhyloP100		-0.0030
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: rs9262492; hg19: chr6-30986015;