ENST00000561567.1:n.95-11274G>A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000260177 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000260177	ENST00000832477.1	n.248-11274G>A		intron_variant	Intron 1 of 1
ENSG00000260177	ENST00000832478.1	n.397-11274G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.863 AC: 35767 AN: 41466

American (AMR) AF: 0.502 AC: 7648 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2098 AN: 3468

East Asian (EAS) AF: 0.476 AC: 2447 AN: 5144

South Asian (SAS) AF: 0.739 AC: 3557 AN: 4816

European-Finnish (FIN) AF: 0.570 AC: 6002 AN: 10536

Middle Eastern (MID) AF: 0.712 AC: 208 AN: 292

European-Non Finnish (NFE) AF: 0.575 AC: 39058 AN: 67950

Other (OTH) AF: 0.644 AC: 1355 AN: 2104

Alfa AF: 0.591 Hom.: 28422

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs8050022; hg19: chr16-87825675;