rs9311810

Variant names:

• chr3-61459532-A-G
• rs9311810

Your query was ambiguous. Multiple possible variants found:

• chr3-61459532-A-G
• chr3-61459532-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.037 in 121,904 control chromosomes in the GnomAD database, including 240 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 0.037 (240 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0370 AC: 4506 AN: 121852 Hom.: 240 Cov.: 26

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0179

Gnomad ASJ AF: 0.000314

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00122

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0227

Gnomad NFE AF: 0.000852

Gnomad OTH AF: 0.0340

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

GnomAD4 genome AF: 0.0370 AC: 4514 AN: 121904 Hom.: 240 Cov.: 26 AF XY: 0.0383 AC XY: 2175 AN XY: 56742

African (AFR) AF: 0.126 AC: 4220 AN: 33420

American (AMR) AF: 0.0177 AC: 179 AN: 10088

Ashkenazi Jewish (ASJ) AF: 0.000314 AC: 1 AN: 3188

East Asian (EAS) AF: 0.00 AC: 0 AN: 4180

South Asian (SAS) AF: 0.00123 AC: 5 AN: 4074

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4554

Middle Eastern (MID) AF: 0.0235 AC: 4 AN: 170

European-Non Finnish (NFE) AF: 0.000852 AC: 51 AN: 59840

Other (OTH) AF: 0.0337 AC: 54 AN: 1604

Alfa AF: 0.0225 Hom.: 23

Bravo AF: 0.0354

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.0
DANN	Benign	0.78
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs9311810; hg19: chr3-61445206;