NM_001318484.1:c.7+1314G>A

Variant names:

• chr6-31007447-G-A
• rs2523924
• NM_001318484.1:c.7+1314G>A

Variant summary

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

The NM_001318484.1(MUC22):​c.7+1314G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,100 control chromosomes in the GnomAD database, including 1,740 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 0.15 (1740 hom., cov: 32)
• Consequence: MUC22 NM_001318484.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.378
• Publications: 13 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318484.1. 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_001318484.1		c.7+1314G>A		intron	N/A	NP_001305413.1
	MUC22	NM_001198815.1		c.-38+1314G>A		intron	N/A	NP_001185744.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22464 AN: 151982 Hom.: 1732 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0953

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.148 AC: 22491 AN: 152100 Hom.: 1740 Cov.: 32 AF XY: 0.146 AC XY: 10880 AN XY: 74368

African (AFR) AF: 0.155 AC: 6408 AN: 41464

American (AMR) AF: 0.201 AC: 3068 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 927 AN: 3466

East Asian (EAS) AF: 0.112 AC: 578 AN: 5180

South Asian (SAS) AF: 0.112 AC: 539 AN: 4822

European-Finnish (FIN) AF: 0.0953 AC: 1009 AN: 10584

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9476 AN: 67998

Other (OTH) AF: 0.169 AC: 356 AN: 2108

Alfa AF: 0.141 Hom.: 2905

Bravo AF: 0.157

Asia WGS AF: 0.151 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.52
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs2523924; hg19: chr6-30975224; COSMIC: COSV73736511;