rs2978041

chr8-133594434-A-C

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 0.345 in 152,120 control chromosomes in the GnomAD database, including 10,772 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 0.34 (10772 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52406 AN: 152002 Hom.: 10743 Cov.: 33

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.345 AC: 52472 AN: 152120 Hom.: 10772 Cov.: 33 AF XY: 0.341 AC XY: 25335 AN XY: 74368

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.311

Alfa AF: 0.279 Hom.: 8137

Bravo AF: 0.345

Asia WGS AF: 0.204 AC: 710 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	0.69
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2978041; hg19: chr8-134606677;