XR_941009.2:n.-154C>T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377187	XR_941009.2	n.-154C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;