12-21240084-T-G

Variant names:

• chr12-21240084-T-G
• rs12372157
• XR_007063239.1:n.87-5785A>C

Variant summary

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

The XR_007063239.1(LOC124902895):​n.87-5785A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,010 control chromosomes in the GnomAD database, including 12,563 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 0.39 (12563 hom., cov: 32)
• Consequence: LOC124902895 XR_007063239.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 7 publications found

Genes affected

LOC124902895 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902895	XR_007063239.1	n.87-5785A>C		intron_variant	Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59899 AN: 151892 Hom.: 12555 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.394 AC: 59938 AN: 152010 Hom.: 12563 Cov.: 32 AF XY: 0.401 AC XY: 29788 AN XY: 74290

African (AFR) AF: 0.287 AC: 11906 AN: 41474

American (AMR) AF: 0.391 AC: 5969 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1627 AN: 3464

East Asian (EAS) AF: 0.734 AC: 3787 AN: 5158

South Asian (SAS) AF: 0.406 AC: 1957 AN: 4822

European-Finnish (FIN) AF: 0.485 AC: 5117 AN: 10554

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28067 AN: 67946

Other (OTH) AF: 0.405 AC: 855 AN: 2112

Alfa AF: 0.407 Hom.: 21333

Bravo AF: 0.387

Asia WGS AF: 0.572 AC: 1990 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	3.6
DANN	Benign	0.46
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs12372157; hg19: chr12-21393018;