rs6473383

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000254394 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254394	ENST00000658531.1	n.254-146770G>A		intron_variant	Intron 3 of 3
ENSG00000254394	ENST00000663058.1	n.943+153255G>A		intron_variant	Intron 6 of 7

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

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.0998

Gnomad4 EAS AF: 0.00734

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.179

Alfa AF: 0.148 Hom.: 3810

Bravo AF: 0.188

Asia WGS AF: 0.130 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6473383; hg19: chr8-83669120;