rs17190071

Variant names:

• chr6-31031926-G-A
• rs17190071
• NM_001395414.1:c.4670-270G>A

Variant summary

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

The NM_001395414.1(MUC22):​c.4670-270G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,024 control chromosomes in the GnomAD database, including 1,106 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 0.11 (1106 hom., cov: 31)
• Consequence: MUC22 NM_001395414.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUC22	NM_001395414.1	c.4670-270G>A		intron_variant	Intron 2 of 3	ENST00000561890.1	NP_001382343.1
MUC22	NM_001318484.1	c.4679-270G>A		intron_variant	Intron 3 of 4		NP_001305413.1
MUC22	NM_001198815.1	c.4670-270G>A		intron_variant	Intron 3 of 4		NP_001185744.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC22	ENST00000561890.1	c.4670-270G>A		intron_variant	Intron 2 of 3	2	NM_001395414.1	ENSP00000455906.1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16663 AN: 151906 Hom.: 1109 Cov.: 31

Gnomad AFR AF: 0.0439

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0536

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.110 AC: 16663 AN: 152024 Hom.: 1106 Cov.: 31 AF XY: 0.114 AC XY: 8438 AN XY: 74292

Gnomad4 AFR AF: 0.0438

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.0538

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.123

Alfa AF: 0.115 Hom.: 263

Bravo AF: 0.102

Asia WGS AF: 0.0800 AC: 279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.14
DANN	Benign	0.52

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: rs17190071; hg19: chr6-30999703;