rs6473383

Positions:

• chr8-82756885-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663058.1(ENSG00000254394):​n.943+153255G>A variant causes a intron, non coding transcript 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: ENST00000663058.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000663058.1	n.943+153255G>A		intron_variant, non_coding_transcript_variant
	ENST00000658531.1	n.254-146770G>A		intron_variant, non_coding_transcript_variant

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;