chr8-66004902-A-G

Variant names:

• chr8-66004902-A-G
• rs2357569
• ENST00000837914.1:n.383+12749T>C

Variant summary

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

The ENST00000837914.1(ENSG00000309029):​n.383+12749T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 152,122 control chromosomes in the GnomAD database, including 21,542 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 0.47 (21542 hom., cov: 32)
• Consequence: ENSG00000309029 ENST00000837914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 1 publications found

Genes affected

ENSG00000309029 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837914.1. 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
	ENSG00000309029	ENST00000837914.1		n.383+12749T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71300 AN: 152002 Hom.: 21491 Cov.: 32

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.469 AC: 71408 AN: 152122 Hom.: 21542 Cov.: 32 AF XY: 0.460 AC XY: 34248 AN XY: 74400

African (AFR) AF: 0.863 AC: 35786 AN: 41488

American (AMR) AF: 0.385 AC: 5886 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1362 AN: 3470

East Asian (EAS) AF: 0.103 AC: 536 AN: 5182

South Asian (SAS) AF: 0.251 AC: 1207 AN: 4814

European-Finnish (FIN) AF: 0.280 AC: 2969 AN: 10598

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22289 AN: 67966

Other (OTH) AF: 0.460 AC: 971 AN: 2112

Alfa AF: 0.421 Hom.: 2241

Bravo AF: 0.494

Asia WGS AF: 0.247 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.54
PhyloP100		-0.48

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: rs2357569;

hg19: chr8-66917137;