rs265318

Variant names:

• chr3-10138975-C-A
• rs265318

Your query was ambiguous. Multiple possible variants found:

• chr3-10138975-C-A
• chr3-10138975-C-G
• chr3-10138975-C-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 0.891 in 152,286 control chromosomes in the GnomAD database, including 60,520 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 0.89 (60520 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.908 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: 0.891 AC: 135571 AN: 152168 Hom.: 60486 Cov.: 34

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.881

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.885

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

GnomAD4 genome AF: 0.891 AC: 135654 AN: 152286 Hom.: 60520 Cov.: 34 AF XY: 0.891 AC XY: 66377 AN XY: 74470

African (AFR) AF: 0.915 AC: 38064 AN: 41578

American (AMR) AF: 0.869 AC: 13262 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3151 AN: 3470

East Asian (EAS) AF: 0.886 AC: 4598 AN: 5192

South Asian (SAS) AF: 0.806 AC: 3890 AN: 4824

European-Finnish (FIN) AF: 0.901 AC: 9565 AN: 10612

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.885 AC: 60210 AN: 68020

Other (OTH) AF: 0.879 AC: 1859 AN: 2116

Alfa AF: 0.887 Hom.: 46799

Bravo AF: 0.891

Asia WGS AF: 0.823 AC: 2865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.58
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs265318; hg19: chr3-10180659;