rs1240083

Variant names:

• chr8-89051573-A-T
• rs1240083

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 0.28 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.296 AC: 12274 AN: 41470

American (AMR) AF: 0.196 AC: 3000 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1198 AN: 3464

East Asian (EAS) AF: 0.187 AC: 969 AN: 5174

South Asian (SAS) AF: 0.359 AC: 1730 AN: 4824

European-Finnish (FIN) AF: 0.332 AC: 3503 AN: 10552

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19022 AN: 67944

Other (OTH) AF: 0.255 AC: 540 AN: 2114

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1240083; hg19: chr8-90063802;