chr8-11587007-G-A

Position:

• chr8-11587007-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 0.539 in 152,028 control chromosomes in the GnomAD database, including 23,115 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 0.54 (23115 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81857 AN: 151910 Hom.: 23086 Cov.: 32

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.539 AC: 81931 AN: 152028 Hom.: 23115 Cov.: 32 AF XY: 0.553 AC XY: 41075 AN XY: 74326

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.991

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.608

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.530

Alfa AF: 0.470 Hom.: 14377

Bravo AF: 0.545

Asia WGS AF: 0.814 AC: 2826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10097870; hg19: chr8-11444516;