8-53252242-C-T

Variant names:

• chr8-53252242-C-T
• rs3808627

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 0.154 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0538 AC: 2233 AN: 41500

American (AMR) AF: 0.218 AC: 3328 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 494 AN: 3340

East Asian (EAS) AF: 0.224 AC: 1156 AN: 5150

South Asian (SAS) AF: 0.147 AC: 697 AN: 4732

European-Finnish (FIN) AF: 0.194 AC: 1948 AN: 10048

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.192 AC: 12939 AN: 67450

Other (OTH) AF: 0.164 AC: 345 AN: 2098

Alfa AF: 0.173 Hom.: 5706

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
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs3808627; hg19: chr8-54164802;