chr8-133956258-G-T

Variant names:

• chr8-133956258-G-T
• rs1503766

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 0.26 in 152,080 control chromosomes in the GnomAD database, including 7,796 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 0.26 (7796 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 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: 0.260 AC: 39531 AN: 151962 Hom.: 7767 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.00731

Gnomad SAS AF: 0.0935

Gnomad FIN AF: 0.0767

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.260 AC: 39593 AN: 152080 Hom.: 7796 Cov.: 32 AF XY: 0.251 AC XY: 18681 AN XY: 74362

African (AFR) AF: 0.552 AC: 22895 AN: 41448

American (AMR) AF: 0.186 AC: 2846 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3468

East Asian (EAS) AF: 0.00733 AC: 38 AN: 5186

South Asian (SAS) AF: 0.0922 AC: 444 AN: 4818

European-Finnish (FIN) AF: 0.0767 AC: 812 AN: 10586

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.164 AC: 11123 AN: 67992

Other (OTH) AF: 0.248 AC: 525 AN: 2116

Alfa AF: 0.193 Hom.: 2942

Bravo AF: 0.280

Asia WGS AF: 0.0890 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.57
PhyloP100		0.075

Splicing

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

Other links and lift over

dbSNP: rs1503766; hg19: chr8-134968501;