rs6511838

Positions:

• chr19-9040162-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.83-4094A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 151,892 control chromosomes in the GnomAD database, including 40,260 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 0.72 (40260 hom., cov: 31)
• Consequence: MUC16 NM_001414686.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.677

Genes affected

MUC16 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUC16	NM_001414686.1	c.83-4094A>G		intron_variant			NP_001401615.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.718 AC: 108909 AN: 151772 Hom.: 40209 Cov.: 31

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.718 AC: 109016 AN: 151892 Hom.: 40260 Cov.: 31 AF XY: 0.714 AC XY: 52993 AN XY: 74182

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.682

Alfa AF: 0.700 Hom.: 3520

Bravo AF: 0.725

Asia WGS AF: 0.559 AC: 1946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.6
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6511838; hg19: chr19-9150838;