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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370082	XR_945558.3	n.891-7288A>G		intron_variant	Intron 2 of 3
LOC105370082	XR_945559.3	n.729-7288A>G		intron_variant	Intron 2 of 3

Ensembl

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

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 v4.3

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;