XR_007096287.1:n.36+12990C>G

Variant names:

• chr3-166114553-C-G
• rs4440084
• XR_007096287.1:n.36+12990C>G

Variant summary

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

The XR_007096287.1(LOC124909497):​n.36+12990C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 151,592 control chromosomes in the GnomAD database, including 27,934 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 0.59 (27934 hom., cov: 30)
• Consequence: LOC124909497 XR_007096287.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578
• Publications: 8 publications found

Genes affected

LOC124909497 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.593 AC: 89798 AN: 151472 Hom.: 27898 Cov.: 30

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.593 AC: 89879 AN: 151592 Hom.: 27934 Cov.: 30 AF XY: 0.591 AC XY: 43732 AN XY: 74026

African (AFR) AF: 0.798 AC: 33031 AN: 41386

American (AMR) AF: 0.501 AC: 7607 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1944 AN: 3470

East Asian (EAS) AF: 0.483 AC: 2476 AN: 5130

South Asian (SAS) AF: 0.406 AC: 1951 AN: 4806

European-Finnish (FIN) AF: 0.537 AC: 5621 AN: 10476

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35281 AN: 67822

Other (OTH) AF: 0.588 AC: 1233 AN: 2098

Alfa AF: 0.461 Hom.: 1377

Bravo AF: 0.603

Asia WGS AF: 0.468 AC: 1628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	3.3
DANN	Benign	0.84
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs4440084; hg19: chr3-165832341;