ENST00000563114.1:n.42-1295T>C

Variant names:

• chr16-78016424-A-G
• rs12597064
• ENST00000563114.1:n.42-1295T>C

Variant summary

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

The ENST00000563114.1(ENSG00000261540):​n.42-1295T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 151,960 control chromosomes in the GnomAD database, including 5,482 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 0.27 (5482 hom., cov: 31)
• Consequence: ENSG00000261540 ENST00000563114.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 4 publications found

Genes affected

ENSG00000261540 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 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
ENSG00000261540	ENST00000563114.1	n.42-1295T>C		intron_variant	Intron 1 of 1	1
ENSG00000261540	ENST00000767192.1	n.291+650T>C		intron_variant	Intron 2 of 2
ENSG00000261540	ENST00000767193.1	n.593+650T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40475 AN: 151844 Hom.: 5468 Cov.: 31

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.267 AC: 40514 AN: 151960 Hom.: 5482 Cov.: 31 AF XY: 0.270 AC XY: 20026 AN XY: 74284

African (AFR) AF: 0.260 AC: 10780 AN: 41444

American (AMR) AF: 0.227 AC: 3458 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 990 AN: 3472

East Asian (EAS) AF: 0.210 AC: 1078 AN: 5140

South Asian (SAS) AF: 0.285 AC: 1370 AN: 4812

European-Finnish (FIN) AF: 0.336 AC: 3544 AN: 10560

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18535 AN: 67958

Other (OTH) AF: 0.241 AC: 508 AN: 2112

Alfa AF: 0.267 Hom.: 9302

Bravo AF: 0.257

Asia WGS AF: 0.223 AC: 773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.70
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12597064; hg19: chr16-78050321;