chr8-133603893-T-G

Variant names:

• chr8-133603893-T-G
• rs2978048

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 0.0515 in 152,252 control chromosomes in the GnomAD database, including 323 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 0.052 (323 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.071 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: 0.0516 AC: 7847 AN: 152134 Hom.: 323 Cov.: 31

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0330

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0776

Gnomad FIN AF: 0.0998

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0712

Gnomad OTH AF: 0.0521

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

GnomAD4 genome AF: 0.0515 AC: 7845 AN: 152252 Hom.: 323 Cov.: 31 AF XY: 0.0526 AC XY: 3918 AN XY: 74432

African (AFR) AF: 0.0118 AC: 491 AN: 41550

American (AMR) AF: 0.0330 AC: 504 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3470

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5180

South Asian (SAS) AF: 0.0775 AC: 374 AN: 4826

European-Finnish (FIN) AF: 0.0998 AC: 1059 AN: 10610

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0712 AC: 4845 AN: 68006

Other (OTH) AF: 0.0516 AC: 109 AN: 2114

Alfa AF: 0.0666 Hom.: 697

Bravo AF: 0.0441

Asia WGS AF: 0.0270 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.42
DANN	Benign	0.66
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2978048; hg19: chr8-134616136;