chr16-78016424-A-G

Position:

• chr16-78016424-A-G

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, non coding transcript 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: ENST00000563114.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000563114.1	n.42-1295T>C		intron_variant, non_coding_transcript_variant		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;