rs16932946

Positions:

• chr11-5564486-C-A

Variant summary

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

The ENST00000380259.7(ENSG00000239920):​n.*739+26339G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,158 control chromosomes in the GnomAD database, including 1,459 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 0.12 (1459 hom., cov: 33)
• Consequence: ENSG00000239920 ENST00000380259.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172

Genes affected

ENSG00000239920 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000239920	ENST00000380259.7	n.*739+26339G>T		intron_variant		5		ENSP00000369609.3

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18755 AN: 152040 Hom.: 1456 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0872

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.0479

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0910

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.123 AC: 18785 AN: 152158 Hom.: 1459 Cov.: 33 AF XY: 0.122 AC XY: 9048 AN XY: 74388

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.0871

Gnomad4 ASJ AF: 0.0841

Gnomad4 EAS AF: 0.0481

Gnomad4 SAS AF: 0.0263

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0910

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0994 Hom.: 536

Bravo AF: 0.130

Asia WGS AF: 0.0600 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.65

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: rs16932946; hg19: chr11-5585716; COSMIC: COSV66627257;