16-78019746-A-T

Position:

• chr16-78019746-A-T

Variant summary

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

The ENST00000563114.1(ENSG00000261540):​n.42-4617T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 152,082 control chromosomes in the GnomAD database, including 32,464 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 0.63 (32464 hom., cov: 32)
• Consequence: ENSG00000261540 ENST00000563114.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146

Genes affected

ENSG00000261540 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.767 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
ENSG00000261540	ENST00000563114.1	n.42-4617T>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95697 AN: 151964 Hom.: 32448 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.630 AC: 95747 AN: 152082 Hom.: 32464 Cov.: 32 AF XY: 0.635 AC XY: 47238 AN XY: 74352

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.692

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.788

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.737

Gnomad4 OTH AF: 0.667

Alfa AF: 0.574 Hom.: 1891

Bravo AF: 0.610

Asia WGS AF: 0.740 AC: 2568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.97
DANN	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2735413; hg19: chr16-78053643;