rs7132674

Variant names:

• chr12-11191389-A-G
• rs7132674
• XR_007063209.1:n.760+1278A>G

Variant summary

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

The XR_007063209.1(LOC107987435):​n.760+1278A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 152,114 control chromosomes in the GnomAD database, including 22,062 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 0.51 (22062 hom., cov: 33)
• Consequence: LOC107987435 XR_007063209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681
• Publications: 22 publications found

Genes affected

LOC107987435 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987435	XR_007063209.1	n.760+1278A>G		intron_variant	Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77147 AN: 151996 Hom.: 22058 Cov.: 33

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.507 AC: 77159 AN: 152114 Hom.: 22062 Cov.: 33 AF XY: 0.515 AC XY: 38297 AN XY: 74370

African (AFR) AF: 0.222 AC: 9223 AN: 41490

American (AMR) AF: 0.597 AC: 9119 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2258 AN: 3468

East Asian (EAS) AF: 0.742 AC: 3827 AN: 5156

South Asian (SAS) AF: 0.649 AC: 3125 AN: 4818

European-Finnish (FIN) AF: 0.666 AC: 7049 AN: 10584

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40583 AN: 67998

Other (OTH) AF: 0.545 AC: 1152 AN: 2112

Alfa AF: 0.563 Hom.: 52687

Bravo AF: 0.491

Asia WGS AF: 0.652 AC: 2265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.42
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs7132674; hg19: chr12-11344304;