chr12-40416791-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_173600.2(MUC19):​c.1321+432C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 151,786 control chromosomes in the GnomAD database, including 24,255 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 0.56 ( 24255 hom., cov: 32)

Consequence

MUC19
NM_173600.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.354
Variant links:
Genes affected
MUC19 (HGNC:14362): (mucin 19, oligomeric) This gene encodes a member of the gel-forming mucin protein family. Mucin family members are glycoproteins that have tandem repeats which are extensively O-glycosylated. The structural features of mucin proteins are responsible for the gel-like properties of mucus. The encoded protein may be involved in disruption of the ocular surface in Sjogren syndrome. [provided by RefSeq, Apr 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MUC19NM_173600.2 linkuse as main transcriptc.1321+432C>T intron_variant
LOC105369736XR_944868.3 linkuse as main transcriptn.167-353G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MUC19ENST00000454784.10 linkuse as main transcriptc.1321+432C>T intron_variant 5 P1
ENST00000552757.1 linkuse as main transcriptn.117+3429G>A intron_variant, non_coding_transcript_variant 5
MUC19ENST00000676020.2 linkuse as main transcriptn.1374+432C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.564
AC:
85507
AN:
151668
Hom.:
24244
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.573
Gnomad AMI
AF:
0.468
Gnomad AMR
AF:
0.534
Gnomad ASJ
AF:
0.532
Gnomad EAS
AF:
0.469
Gnomad SAS
AF:
0.619
Gnomad FIN
AF:
0.528
Gnomad MID
AF:
0.424
Gnomad NFE
AF:
0.578
Gnomad OTH
AF:
0.555
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.564
AC:
85566
AN:
151786
Hom.:
24255
Cov.:
32
AF XY:
0.564
AC XY:
41790
AN XY:
74150
show subpopulations
Gnomad4 AFR
AF:
0.573
Gnomad4 AMR
AF:
0.534
Gnomad4 ASJ
AF:
0.532
Gnomad4 EAS
AF:
0.468
Gnomad4 SAS
AF:
0.618
Gnomad4 FIN
AF:
0.528
Gnomad4 NFE
AF:
0.578
Gnomad4 OTH
AF:
0.552
Alfa
AF:
0.569
Hom.:
32763
Bravo
AF:
0.557
Asia WGS
AF:
0.511
AC:
1775
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.56
DANN
Benign
0.55

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1820545; hg19: chr12-40810593; API