rs1982229

chr8-27617082-C-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 0.293 in 152,122 control chromosomes in the GnomAD database, including 7,213 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 0.29 (7213 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.811

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.362 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: 0.293 AC: 44532 AN: 152004 Hom.: 7206 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.293 AC: 44567 AN: 152122 Hom.: 7213 Cov.: 32 AF XY: 0.294 AC XY: 21866 AN XY: 74350

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.292

Alfa AF: 0.311 Hom.: 1163

Bravo AF: 0.281

Asia WGS AF: 0.255 AC: 887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.76
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1982229; hg19: chr8-27474599;