rs7296239

Variant names:

• chr12-54197920-T-C
• rs7296239
• XR_944983.1:n.367-2540T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-54197920-T-C
• chr12-54197920-T-G

Variant summary

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

The XR_944983.1(LOC105369777):​n.367-2540T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 151,782 control chromosomes in the GnomAD database, including 14,735 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 0.42 (14735 hom., cov: 30)
• Consequence: LOC105369777 XR_944983.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 14 publications found

Genes affected

LOC105369777 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 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: 0.423 AC: 64164 AN: 151666 Hom.: 14711 Cov.: 30

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.423 AC: 64217 AN: 151782 Hom.: 14735 Cov.: 30 AF XY: 0.430 AC XY: 31888 AN XY: 74142

African (AFR) AF: 0.592 AC: 24479 AN: 41384

American (AMR) AF: 0.367 AC: 5597 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1307 AN: 3470

East Asian (EAS) AF: 0.528 AC: 2717 AN: 5144

South Asian (SAS) AF: 0.549 AC: 2643 AN: 4818

European-Finnish (FIN) AF: 0.452 AC: 4736 AN: 10478

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21541 AN: 67922

Other (OTH) AF: 0.372 AC: 784 AN: 2106

Alfa AF: 0.351 Hom.: 40736

Bravo AF: 0.421

Asia WGS AF: 0.513 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.3
DANN	Benign	0.55
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs7296239; hg19: chr12-54591704;