chr8-82847327-G-A

Variant names:

• chr8-82847327-G-A
• rs16919696
• ENST00000658531.1:n.254-56328G>A

Variant summary

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

The ENST00000658531.1(ENSG00000254394):​n.254-56328G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0553 in 86,686 control chromosomes in the GnomAD database, including 257 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 0.055 (257 hom., cov: 30)
• Consequence: ENSG00000254394 ENST00000658531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318
• Publications: 0 publications found

Genes affected

ENSG00000254394 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658531.1. 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
	ENSG00000254394	ENST00000658531.1		n.254-56328G>A		intron	N/A
	ENSG00000254394	ENST00000663058.1		n.944-65612G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0554 AC: 4795 AN: 86624 Hom.: 258 Cov.: 30

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0339

Gnomad ASJ AF: 0.000831

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00168

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00450

Gnomad NFE AF: 0.00101

Gnomad OTH AF: 0.0492

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

GnomAD4 genome AF: 0.0553 AC: 4794 AN: 86686 Hom.: 257 Cov.: 30 AF XY: 0.0539 AC XY: 2277 AN XY: 42252

African (AFR) AF: 0.171 AC: 4432 AN: 25852

American (AMR) AF: 0.0338 AC: 258 AN: 7622

Ashkenazi Jewish (ASJ) AF: 0.000831 AC: 2 AN: 2408

East Asian (EAS) AF: 0.00 AC: 0 AN: 2238

South Asian (SAS) AF: 0.00126 AC: 3 AN: 2388

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5626

Middle Eastern (MID) AF: 0.00485 AC: 1 AN: 206

European-Non Finnish (NFE) AF: 0.00101 AC: 39 AN: 38662

Other (OTH) AF: 0.0491 AC: 59 AN: 1202

Alfa AF: 0.00475 Hom.: 7

Bravo AF: 0.0373

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.58
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs16919696; hg19: chr8-83759562;