rs8049365

Variant names:

• chr16-76785421-C-T
• rs8049365
• ENST00000563764.2:n.*123-34165C>T

Variant summary

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

The ENST00000563764.2(ENSG00000287694):​n.*123-34165C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,042 control chromosomes in the GnomAD database, including 9,492 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 0.35 (9492 hom., cov: 33)
• Consequence: ENSG00000287694 ENST00000563764.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737

Genes affected

ENSG00000287694 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.395 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.*123-34165C>T		intron_variant	Intron 3 of 3	3		ENSP00000455258.1
ENSG00000259995	ENST00000567777.1	n.138+48942C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52935 AN: 151926 Hom.: 9475 Cov.: 33

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.348 AC: 52985 AN: 152042 Hom.: 9492 Cov.: 33 AF XY: 0.349 AC XY: 25954 AN XY: 74314

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.352

Alfa AF: 0.342 Hom.: 1530

Bravo AF: 0.357

Asia WGS AF: 0.374 AC: 1300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.88
DANN	Benign	0.74

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: rs8049365; hg19: chr16-76819318;