rs1240083

Positions:

• chr8-89051573-A-T

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 0.28 in 152,018 control chromosomes in the GnomAD database, including 6,167 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 0.28 (6167 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

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 (SAS) allele frequency at 95% confidence interval = 0.345 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: 0.280 AC: 42594 AN: 151900 Hom.: 6156 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.280 AC: 42638 AN: 152018 Hom.: 6167 Cov.: 32 AF XY: 0.282 AC XY: 20973 AN XY: 74308

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.255

Alfa AF: 0.174 Hom.: 358

Bravo AF: 0.269

Asia WGS AF: 0.265 AC: 919 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1240083; hg19: chr8-90063802;