rs2978387

Positions:

• chr8-144923262-A-G

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 0.277 in 152,078 control chromosomes in the GnomAD database, including 5,906 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 0.28 (5906 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42142 AN: 151960 Hom.: 5898 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.277 AC: 42183 AN: 152078 Hom.: 5906 Cov.: 32 AF XY: 0.280 AC XY: 20832 AN XY: 74328

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.292

Alfa AF: 0.263 Hom.: 676

Bravo AF: 0.274

Asia WGS AF: 0.348 AC: 1210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2978387; hg19: chr8-146148648;