8-133449608-A-G

Variant names:

• chr8-133449608-A-G
• rs10106540

Variant summary

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

The variant allele was found at a frequency of 0.375 in 152,098 control chromosomes in the GnomAD database, including 11,667 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 0.37 (11667 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 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

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56925 AN: 151980 Hom.: 11657 Cov.: 33

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.375 AC: 56972 AN: 152098 Hom.: 11667 Cov.: 33 AF XY: 0.373 AC XY: 27766 AN XY: 74364

African (AFR) AF: 0.541 AC: 22419 AN: 41446

American (AMR) AF: 0.305 AC: 4669 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1028 AN: 3468

East Asian (EAS) AF: 0.505 AC: 2610 AN: 5168

South Asian (SAS) AF: 0.390 AC: 1879 AN: 4824

European-Finnish (FIN) AF: 0.313 AC: 3316 AN: 10588

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19855 AN: 67988

Other (OTH) AF: 0.373 AC: 790 AN: 2116

Alfa AF: 0.311 Hom.: 6286

Bravo AF: 0.384

Asia WGS AF: 0.426 AC: 1483 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	0.20
DANN	Benign	0.48
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10106540; hg19: chr8-134461851;