rs9871760

Variant names:

• chr3-127274256-C-A
• rs9871760

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 0.279 in 152,098 control chromosomes in the GnomAD database, including 6,506 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 0.28 (6506 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.585 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: 0.280 AC: 42495 AN: 151980 Hom.: 6506 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.279 AC: 42511 AN: 152098 Hom.: 6506 Cov.: 33 AF XY: 0.289 AC XY: 21487 AN XY: 74374

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.244

Alfa AF: 0.242 Hom.: 5114

Bravo AF: 0.283

Asia WGS AF: 0.460 AC: 1595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.6
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9871760; hg19: chr3-126993099;