rs8049894

Variant names:

• chr16-76780487-G-C
• rs8049894
• ENST00000563764.2:n.*123-39099G>C

Variant summary

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

The ENST00000563764.2(ENSG00000287694):​n.*123-39099G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 151,952 control chromosomes in the GnomAD database, including 3,638 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 0.21 (3638 hom., cov: 32)
• Consequence: ENSG00000287694 ENST00000563764.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.644

Genes affected

ENSG00000287694 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 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
ENSG00000287694	ENST00000563764.2	n.*123-39099G>C		intron_variant	Intron 3 of 3	3		ENSP00000455258.1
ENSG00000259995	ENST00000567777.1	n.138+44008G>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32048 AN: 151832 Hom.: 3625 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.211 AC: 32080 AN: 151952 Hom.: 3638 Cov.: 32 AF XY: 0.211 AC XY: 15638 AN XY: 74266

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.199

Alfa AF: 0.201 Hom.: 424

Bravo AF: 0.210

Asia WGS AF: 0.244 AC: 851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.5
DANN	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs8049894; hg19: chr16-76814384;