8-16787646-T-A

Variant names:

• chr8-16787646-T-A
• rs6992112
• ENST00000521411.2:n.279-4364A>T

Variant summary

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

The ENST00000521411.2(ENSG00000253496):​n.279-4364A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.904 in 152,214 control chromosomes in the GnomAD database, including 62,798 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 0.90 (62798 hom., cov: 32)
• Consequence: ENSG00000253496 ENST00000521411.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 0 publications found

Genes affected

ENSG00000253496 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521411.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253496	ENST00000521411.2	TSL:5	n.279-4364A>T		intron	N/A
	ENSG00000253496	ENST00000755781.1		n.229-4364A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.904 AC: 137541 AN: 152096 Hom.: 62783 Cov.: 32

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.942

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.926

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

GnomAD4 genome AF: 0.904 AC: 137604 AN: 152214 Hom.: 62798 Cov.: 32 AF XY: 0.904 AC XY: 67303 AN XY: 74418

African (AFR) AF: 0.771 AC: 31983 AN: 41496

American (AMR) AF: 0.942 AC: 14405 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3292 AN: 3472

East Asian (EAS) AF: 0.858 AC: 4437 AN: 5170

South Asian (SAS) AF: 0.919 AC: 4440 AN: 4830

European-Finnish (FIN) AF: 0.963 AC: 10217 AN: 10610

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.966 AC: 65703 AN: 68040

Other (OTH) AF: 0.928 AC: 1961 AN: 2114

Alfa AF: 0.928 Hom.: 8192

Bravo AF: 0.896

Asia WGS AF: 0.903 AC: 3140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.8
DANN	Benign	0.81
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs6992112; hg19: chr8-16645155;