rs9310862

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;