chr8-8689338-G-A

Position:

• chr8-8689338-G-A

Variant summary

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

The variant allele was found at a frequency of 0.316 in 152,066 control chromosomes in the GnomAD database, including 8,080 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 0.32 (8080 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 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

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47971 AN: 151948 Hom.: 8078 Cov.: 33

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.0621

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.316 AC: 47985 AN: 152066 Hom.: 8080 Cov.: 33 AF XY: 0.308 AC XY: 22861 AN XY: 74324

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.0620

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.326

Alfa AF: 0.339 Hom.: 5183

Bravo AF: 0.308

Asia WGS AF: 0.147 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs940031; hg19: chr8-8546848;