rs1710879

chr3-10987735-T-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 0.225 in 149,392 control chromosomes in the GnomAD database, including 4,465 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 0.22 (4465 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.78

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 (SAS) allele frequency at 95% confidence interval = 0.361 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: 0.225 AC: 33603 AN: 149274 Hom.: 4472 Cov.: 31

Gnomad AFR AF: 0.0727

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.225 AC: 33594 AN: 149392 Hom.: 4465 Cov.: 31 AF XY: 0.227 AC XY: 16604 AN XY: 73006

Gnomad4 AFR AF: 0.0725

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.251

Alfa AF: 0.267 Hom.: 2916

Bravo AF: 0.216

Asia WGS AF: 0.290 AC: 1010 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	0.0040
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1710879; hg19: chr3-11029421;