rs2675680

Variant names:

• chr10-73899106-T-C
• rs2675680

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 0.436 in 152,134 control chromosomes in the GnomAD database, including 16,053 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 0.44 (16053 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 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: 0.436 AC: 66322 AN: 152016 Hom.: 16048 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.436 AC: 66344 AN: 152134 Hom.: 16053 Cov.: 32 AF XY: 0.430 AC XY: 32008 AN XY: 74386

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.506

Alfa AF: 0.482 Hom.: 2328

Bravo AF: 0.426

Asia WGS AF: 0.213 AC: 739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2675680; hg19: chr10-75658864;