chr19-9032249-T-C

Position:

• chr19-9032249-T-C

Variant summary

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

The NM_001414686.1(MUC16):​c.514+3388A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,250 control chromosomes in the GnomAD database, including 1,035 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 (1035 hom., cov: 32)
• Consequence: MUC16 NM_001414686.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

Genes affected

MUC16 (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 (SAS) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUC16	NM_001414686.1	c.514+3388A>G		intron_variant			NP_001401615.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17157 AN: 152132 Hom.: 1036 Cov.: 32

Gnomad AFR AF: 0.0900

Gnomad AMI AF: 0.0670

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.113 AC: 17162 AN: 152250 Hom.: 1035 Cov.: 32 AF XY: 0.114 AC XY: 8483 AN XY: 74434

Gnomad4 AFR AF: 0.0901

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.115

Alfa AF: 0.119 Hom.: 1036

Bravo AF: 0.110

Asia WGS AF: 0.133 AC: 464 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	0.65
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8100377; hg19: chr19-9142925;