3-65306814-T-G

Variant names:

• chr3-65306814-T-G
• rs4688557
• XR_001740740.1:n.1189+4666A>C

Variant summary

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

The XR_001740740.1(LOC107986094):​n.1189+4666A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.872 in 152,094 control chromosomes in the GnomAD database, including 58,468 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 0.87 (58468 hom., cov: 31)
• Consequence: LOC107986094 XR_001740740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 1 publications found

Genes affected

LOC107986094 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.947 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: 0.872 AC: 132479 AN: 151976 Hom.: 58435 Cov.: 31

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.915

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.949

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.953

Gnomad OTH AF: 0.889

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

GnomAD4 genome AF: 0.872 AC: 132565 AN: 152094 Hom.: 58468 Cov.: 31 AF XY: 0.868 AC XY: 64512 AN XY: 74332

African (AFR) AF: 0.760 AC: 31483 AN: 41432

American (AMR) AF: 0.792 AC: 12103 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.954 AC: 3309 AN: 3468

East Asian (EAS) AF: 0.779 AC: 4004 AN: 5142

South Asian (SAS) AF: 0.789 AC: 3804 AN: 4822

European-Finnish (FIN) AF: 0.949 AC: 10065 AN: 10604

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.953 AC: 64806 AN: 68024

Other (OTH) AF: 0.889 AC: 1877 AN: 2112

Alfa AF: 0.915 Hom.: 166757

Bravo AF: 0.853

Asia WGS AF: 0.785 AC: 2731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.29
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs4688557; hg19: chr3-65292489;