rs12597064

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr16-78016424-A-G
• chr16-78016424-A-T

Variant summary

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

The ENST00000563114.1(ENSG00000261540):​n.42-1295T>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

Genes affected

ENSG00000261540 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.241

Alfa AF: 0.267 Hom.: 7295

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12597064; hg19: chr16-78050321;