rs1982229

Variant names:

• chr8-27617082-C-T
• rs1982229

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 0.293 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
• Publications: 3 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.166 AC: 6888 AN: 41530

American (AMR) AF: 0.316 AC: 4829 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 909 AN: 3468

East Asian (EAS) AF: 0.160 AC: 826 AN: 5172

South Asian (SAS) AF: 0.300 AC: 1445 AN: 4816

European-Finnish (FIN) AF: 0.366 AC: 3860 AN: 10554

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24866 AN: 67988

Other (OTH) AF: 0.292 AC: 617 AN: 2110

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
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs1982229; hg19: chr8-27474599;