rs9814870

Variant names:

• chr3-95969999-A-G
• rs9814870

Your query was ambiguous. Multiple possible variants found:

• chr3-95969999-A-G
• chr3-95969999-A-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 0.191 in 151,852 control chromosomes in the GnomAD database, including 3,031 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 0.19 (3031 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 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: 0.191 AC: 29029 AN: 151734 Hom.: 3031 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.0782

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.191 AC: 29039 AN: 151852 Hom.: 3031 Cov.: 32 AF XY: 0.193 AC XY: 14307 AN XY: 74196

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.185

Alfa AF: 0.223 Hom.: 8637

Bravo AF: 0.177

Asia WGS AF: 0.230 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9814870; hg19: chr3-95688843;