rs6473383

Variant names:

• chr8-82756885-G-A
• rs6473383
• ENST00000658531.1:n.254-146770G>A

Variant summary

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

The ENST00000658531.1(ENSG00000254394):​n.254-146770G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,002 control chromosomes in the GnomAD database, including 3,207 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 0.19 (3207 hom., cov: 32)
• Consequence: ENSG00000254394 ENST00000658531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254
• Publications: 10 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 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.254-146770G>A		intron	N/A
	ENSG00000254394	ENST00000663058.1		n.943+153255G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28408 AN: 151884 Hom.: 3202 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.0507

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0998

Gnomad EAS AF: 0.00751

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.187 AC: 28433 AN: 152002 Hom.: 3207 Cov.: 32 AF XY: 0.184 AC XY: 13656 AN XY: 74286

African (AFR) AF: 0.307 AC: 12724 AN: 41426

American (AMR) AF: 0.135 AC: 2065 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0998 AC: 346 AN: 3466

East Asian (EAS) AF: 0.00734 AC: 38 AN: 5180

South Asian (SAS) AF: 0.208 AC: 1004 AN: 4822

European-Finnish (FIN) AF: 0.149 AC: 1577 AN: 10558

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.150 AC: 10217 AN: 67956

Other (OTH) AF: 0.179 AC: 377 AN: 2112

Alfa AF: 0.151 Hom.: 5152

Bravo AF: 0.188

Asia WGS AF: 0.130 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.77
DANN	Benign	0.68
PhyloP100		-0.25

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: rs6473383;

hg19: chr8-83669120;