rs1710879

Variant names:

• chr3-10987735-T-C
• rs1710879

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0725 AC: 2888 AN: 39860

American (AMR) AF: 0.285 AC: 4320 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1247 AN: 3450

East Asian (EAS) AF: 0.283 AC: 1432 AN: 5060

South Asian (SAS) AF: 0.376 AC: 1735 AN: 4618

European-Finnish (FIN) AF: 0.226 AC: 2376 AN: 10508

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18652 AN: 67452

Other (OTH) AF: 0.251 AC: 524 AN: 2090

Alfa AF: 0.268 Hom.: 3222

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
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs1710879; hg19: chr3-11029421;