16-31346489-C-T

Variant names:

• chr16-31346489-C-T
• rs11150613
• ENST00000777754.1:n.570+3563G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000777754.1(ENSG00000289930):​n.570+3563G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 152,098 control chromosomes in the GnomAD database, including 41,048 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 0.73 (41048 hom., cov: 32)
• Consequence: ENSG00000289930 ENST00000777754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 9 publications found

Genes affected

ENSG00000289930 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000777754.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289930	ENST00000777754.1		n.570+3563G>A		intron	N/A
	ENSG00000289930	ENST00000777755.1		n.528+3563G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110176 AN: 151980 Hom.: 41005 Cov.: 32

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.725 AC: 110273 AN: 152098 Hom.: 41048 Cov.: 32 AF XY: 0.716 AC XY: 53271 AN XY: 74356

African (AFR) AF: 0.900 AC: 37370 AN: 41516

American (AMR) AF: 0.605 AC: 9227 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2804 AN: 3470

East Asian (EAS) AF: 0.698 AC: 3610 AN: 5170

South Asian (SAS) AF: 0.462 AC: 2229 AN: 4828

European-Finnish (FIN) AF: 0.598 AC: 6327 AN: 10572

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.682 AC: 46331 AN: 67964

Other (OTH) AF: 0.735 AC: 1553 AN: 2112

Alfa AF: 0.731 Hom.: 5880

Bravo AF: 0.739

Asia WGS AF: 0.588 AC: 2043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.38
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs11150613; hg19: chr16-31357810;