rs2978041

Variant names:

• chr8-133594434-A-C
• rs2978041

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;