chr3-83857653-G-A

Variant names:

• chr3-83857653-G-A
• rs4396907
• XR_941009.2:n.-154C>T

Variant summary

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

The XR_941009.2(LOC105377187):​n.-154C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 151,962 control chromosomes in the GnomAD database, including 40,907 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 0.73 (40907 hom., cov: 32)
• Consequence: LOC105377187 XR_941009.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 0 publications found

Genes affected

LOC105377187 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 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: 0.731 AC: 110968 AN: 151846 Hom.: 40857 Cov.: 32

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.731 AC: 111075 AN: 151962 Hom.: 40907 Cov.: 32 AF XY: 0.736 AC XY: 54636 AN XY: 74284

African (AFR) AF: 0.715 AC: 29653 AN: 41500

American (AMR) AF: 0.764 AC: 11658 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2395 AN: 3466

East Asian (EAS) AF: 0.971 AC: 5028 AN: 5176

South Asian (SAS) AF: 0.675 AC: 3261 AN: 4828

European-Finnish (FIN) AF: 0.746 AC: 7879 AN: 10558

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48715 AN: 67866

Other (OTH) AF: 0.748 AC: 1577 AN: 2108

Alfa AF: 0.723 Hom.: 6166

Bravo AF: 0.736

Asia WGS AF: 0.838 AC: 2911 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.64
DANN	Benign	0.32
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs4396907; hg19: chr3-83906804;