chr8-21086875-C-T

Variant names:

• chr8-21086875-C-T
• rs6986709
• ENST00000518967.2:n.246-26940G>A

Variant summary

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

The ENST00000518967.2(ENSG00000254092):​n.246-26940G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0986 in 152,202 control chromosomes in the GnomAD database, including 880 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 0.099 (880 hom., cov: 32)
• Consequence: ENSG00000254092 ENST00000518967.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 2 publications found

Genes affected

ENSG00000254092 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518967.2. 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
	ENSG00000254092	ENST00000518967.2	TSL:2	n.246-26940G>A		intron	N/A
	ENSG00000254092	ENST00000657283.1		n.2094+21959G>A		intron	N/A
	ENSG00000254092	ENST00000657734.1		n.1327-26940G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0986 AC: 14990 AN: 152084 Hom.: 879 Cov.: 32

Gnomad AFR AF: 0.0723

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0956

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.0676

Gnomad FIN AF: 0.0668

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.0986 AC: 15002 AN: 152202 Hom.: 880 Cov.: 32 AF XY: 0.0960 AC XY: 7141 AN XY: 74406

African (AFR) AF: 0.0726 AC: 3015 AN: 41530

American (AMR) AF: 0.0954 AC: 1457 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 612 AN: 3470

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5174

South Asian (SAS) AF: 0.0664 AC: 320 AN: 4816

European-Finnish (FIN) AF: 0.0668 AC: 709 AN: 10608

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8494 AN: 68006

Other (OTH) AF: 0.128 AC: 270 AN: 2112

Alfa AF: 0.120 Hom.: 1545

Bravo AF: 0.101

Asia WGS AF: 0.0370 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.42
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs6986709; hg19: chr8-20944386;