12-131245772-T-G

Variant names:

• chr12-131245772-T-G
• rs4387437
• XR_945558.3:n.891-6870A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_945558.3(LOC105370082):​n.891-6870A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 151,470 control chromosomes in the GnomAD database, including 28,795 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 0.61 (28795 hom., cov: 33)
• Consequence: LOC105370082 XR_945558.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346

Genes affected

LOC105370082 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.23).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370082	XR_945558.3	n.891-6870A>C		intron_variant	Intron 2 of 3
LOC105370082	XR_945559.3	n.729-6870A>C		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92392 AN: 151352 Hom.: 28732 Cov.: 33

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.657

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.611 AC: 92516 AN: 151470 Hom.: 28795 Cov.: 33 AF XY: 0.607 AC XY: 44948 AN XY: 74030

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.615

Alfa AF: 0.587 Hom.: 45921

Bravo AF: 0.625

Asia WGS AF: 0.504 AC: 1756 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	0.54
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4387437; hg19: chr12-131730317;