chr8-133995424-C-T

Variant names:

• chr8-133995424-C-T
• rs6982411
• ENST00000846273.1:n.270-4359G>A

Variant summary

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

The ENST00000846273.1(ENSG00000309969):​n.270-4359G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 151,974 control chromosomes in the GnomAD database, including 23,529 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 0.55 (23529 hom., cov: 32)
• Consequence: ENSG00000309969 ENST00000846273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 4 publications found

Genes affected

ENSG00000309969 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846273.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309969	ENST00000846273.1		n.270-4359G>A		intron	N/A
	ENSG00000309969	ENST00000846274.1		n.114-4359G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83015 AN: 151856 Hom.: 23503 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.547 AC: 83080 AN: 151974 Hom.: 23529 Cov.: 32 AF XY: 0.539 AC XY: 40008 AN XY: 74252

African (AFR) AF: 0.690 AC: 28596 AN: 41452

American (AMR) AF: 0.479 AC: 7320 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1996 AN: 3470

East Asian (EAS) AF: 0.308 AC: 1591 AN: 5170

South Asian (SAS) AF: 0.336 AC: 1619 AN: 4814

European-Finnish (FIN) AF: 0.444 AC: 4684 AN: 10542

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35288 AN: 67946

Other (OTH) AF: 0.574 AC: 1212 AN: 2112

Alfa AF: 0.533 Hom.: 36517

Bravo AF: 0.558

Asia WGS AF: 0.308 AC: 1072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.30
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs6982411; hg19: chr8-135007667;