3-140821876-A-G

Variant names:

• chr3-140821876-A-G
• rs908821

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 0.302 in 152,048 control chromosomes in the GnomAD database, including 7,010 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 0.30 (7010 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215

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 (EAS) allele frequency at 95% confidence interval = 0.427 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: 0.302 AC: 45849 AN: 151930 Hom.: 7008 Cov.: 31

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.302 AC: 45869 AN: 152048 Hom.: 7010 Cov.: 31 AF XY: 0.304 AC XY: 22620 AN XY: 74310

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.296

Alfa AF: 0.293 Hom.: 14340

Bravo AF: 0.303

Asia WGS AF: 0.362 AC: 1256 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	5.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs908821; hg19: chr3-140540718;