rs7488647

Variant names:

• chr12-131246190-T-C
• rs7488647
• XR_945558.3:n.891-7288A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-131246190-T-C
• chr12-131246190-T-G

Variant summary

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

The XR_945558.3(LOC105370082):​n.891-7288A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 151,812 control chromosomes in the GnomAD database, including 31,658 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 0.63 (31658 hom., cov: 31)
• Consequence: LOC105370082 XR_945558.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 1 publications found

Genes affected

LOC105370082 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.24).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.777 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: 0.634 AC: 96203 AN: 151694 Hom.: 31596 Cov.: 31

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.635 AC: 96326 AN: 151812 Hom.: 31658 Cov.: 31 AF XY: 0.629 AC XY: 46674 AN XY: 74158

African (AFR) AF: 0.784 AC: 32479 AN: 41444

American (AMR) AF: 0.667 AC: 10151 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2022 AN: 3470

East Asian (EAS) AF: 0.361 AC: 1858 AN: 5150

South Asian (SAS) AF: 0.610 AC: 2922 AN: 4792

European-Finnish (FIN) AF: 0.467 AC: 4927 AN: 10540

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39867 AN: 67874

Other (OTH) AF: 0.631 AC: 1331 AN: 2108

Alfa AF: 0.603 Hom.: 34761

Bravo AF: 0.655

Asia WGS AF: 0.509 AC: 1773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	1.3
DANN	Benign	0.15
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs7488647; hg19: chr12-131730735;