chr12-40400191-C-T

Position:

• chr12-40400191-C-T

Variant summary

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

The NM_173600.2(MUC19):​c.112+124C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 464,796 control chromosomes in the GnomAD database, including 34,180 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 (11788 hom., cov: 32)
  • Exomes 𝑓: 0.37 (22392 hom.)
• Consequence: MUC19 NM_173600.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUC19	NM_173600.2	c.112+124C>T		intron_variant			NP_775871.2
LOC105369736	XR_944868.3	n.305-1527G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MUC19	ENST00000454784.10	c.112+124C>T		intron_variant		5		ENSP00000508949	P1
	ENST00000552757.1	n.118-1527G>A		intron_variant, non_coding_transcript_variant		5
MUC19	ENST00000676020.2	n.165+124C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59711 AN: 151792 Hom.: 11788 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.387

GnomAD4 exome AF: 0.373 AC: 116762 AN: 312886 Hom.: 22392 AF XY: 0.374 AC XY: 64155 AN XY: 171490

Gnomad4 AFR exome AF: 0.397

Gnomad4 AMR exome AF: 0.337

Gnomad4 ASJ exome AF: 0.376

Gnomad4 EAS exome AF: 0.454

Gnomad4 SAS exome AF: 0.374

Gnomad4 FIN exome AF: 0.380

Gnomad4 NFE exome AF: 0.373

Gnomad4 OTH exome AF: 0.369

GnomAD4 genome AF: 0.393 AC: 59745 AN: 151910 Hom.: 11788 Cov.: 32 AF XY: 0.396 AC XY: 29380 AN XY: 74236

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.386

Alfa AF: 0.360 Hom.: 4480

Bravo AF: 0.392

Asia WGS AF: 0.406 AC: 1407 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1820544; hg19: chr12-40793993;