chr8-77899854-C-T

Variant names:

• chr8-77899854-C-T
• rs10091852
• ENST00000730975.1:n.479-9555G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000730975.1(ENSG00000295568):​n.479-9555G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 151,962 control chromosomes in the GnomAD database, including 4,066 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 (4066 hom., cov: 31)
• Consequence: ENSG00000295568 ENST00000730975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 2 publications found

Genes affected

ENSG00000295568 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730975.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295568	ENST00000730975.1		n.479-9555G>A		intron	N/A
	ENSG00000295568	ENST00000730976.1		n.429-9555G>A		intron	N/A
	ENSG00000295568	ENST00000730977.1		n.504-9555G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32337 AN: 151842 Hom.: 4052 Cov.: 31

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.213 AC: 32381 AN: 151962 Hom.: 4066 Cov.: 31 AF XY: 0.211 AC XY: 15634 AN XY: 74266

African (AFR) AF: 0.347 AC: 14375 AN: 41400

American (AMR) AF: 0.190 AC: 2908 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 648 AN: 3470

East Asian (EAS) AF: 0.114 AC: 585 AN: 5142

South Asian (SAS) AF: 0.264 AC: 1267 AN: 4794

European-Finnish (FIN) AF: 0.116 AC: 1223 AN: 10586

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10666 AN: 67984

Other (OTH) AF: 0.215 AC: 452 AN: 2106

Alfa AF: 0.183 Hom.: 1547

Bravo AF: 0.222

Asia WGS AF: 0.252 AC: 877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.8
DANN	Benign	0.55
PhyloP100		0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10091852;

hg19: chr8-78812089;