8-53252242-C-T

Variant names:

• chr8-53252242-C-T
• rs3808627

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 0.154 in 150,758 control chromosomes in the GnomAD database, including 2,157 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 0.15 (2157 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.214 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: 0.154 AC: 23268 AN: 150640 Hom.: 2158 Cov.: 32

Gnomad AFR AF: 0.0539

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.160

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.154 AC: 23271 AN: 150758 Hom.: 2157 Cov.: 32 AF XY: 0.157 AC XY: 11515 AN XY: 73536

Gnomad4 AFR AF: 0.0538

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.164

Alfa AF: 0.183 Hom.: 3671

Bravo AF: 0.152

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3808627; hg19: chr8-54164802;