rs9310862

Variant names:

• chr3-28165386-G-A
• rs9310862

Your query was ambiguous. Multiple possible variants found:

• chr3-28165386-G-A
• chr3-28165386-G-C
• chr3-28165386-G-T

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 0.483 in 152,000 control chromosomes in the GnomAD database, including 17,825 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 0.48 (17825 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 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: 0.483 AC: 73340 AN: 151882 Hom.: 17817 Cov.: 32

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.483 AC: 73384 AN: 152000 Hom.: 17825 Cov.: 32 AF XY: 0.482 AC XY: 35840 AN XY: 74296

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.521

Alfa AF: 0.493 Hom.: 9773

Bravo AF: 0.487

Asia WGS AF: 0.588 AC: 2045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.085
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9310862; hg19: chr3-28206877;