chr16-87792069-C-T

Variant names:

• chr16-87792069-C-T
• rs8050022
• ENST00000561567.1:n.95-11274G>A

Variant summary

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

The ENST00000561567.1(ENSG00000260177):​n.95-11274G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 151,924 control chromosomes in the GnomAD database, including 33,685 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 0.65 (33685 hom., cov: 30)
• Consequence: ENSG00000260177 ENST00000561567.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

ENSG00000260177 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 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
ENSG00000260177	ENST00000561567.1	n.95-11274G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98593 AN: 151808 Hom.: 33632 Cov.: 30

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.650 AC: 98694 AN: 151924 Hom.: 33685 Cov.: 30 AF XY: 0.646 AC XY: 47934 AN XY: 74230

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.739

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.644

Alfa AF: 0.578 Hom.: 20556

Bravo AF: 0.647

Asia WGS AF: 0.616 AC: 2142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.47
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8050022; hg19: chr16-87825675;