rs2789679

chr10-80148128-A-T

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 0.372 in 152,190 control chromosomes in the GnomAD database, including 11,501 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 0.37 (11501 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 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: 0.372 AC: 56594 AN: 152072 Hom.: 11502 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.372 AC: 56581 AN: 152190 Hom.: 11501 Cov.: 33 AF XY: 0.375 AC XY: 27872 AN XY: 74404

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.394

Alfa AF: 0.388 Hom.: 1582

Bravo AF: 0.362

Asia WGS AF: 0.421 AC: 1461 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	2.9
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2789679; hg19: chr10-81907884;