rs16932946

Variant names:

• chr11-5564486-C-A
• rs16932946
• ENST00000380259.7:n.*739+26339G>T

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000239920	ENST00000380259.7	n.*739+26339G>T		intron_variant	Intron 5 of 7	5		ENSP00000369609.3
ENSG00000290653	ENST00000641694.1	n.*159C>A		downstream_gene_variant
ENSG00000290653	ENST00000641744.1	n.*159C>A		downstream_gene_variant

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;