chr12-71017781-T-G

Variant names:

• chr12-71017781-T-G
• rs7132840
• ENST00000552098.1:n.273+2917A>C

Variant summary

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

The ENST00000552098.1(ENSG00000257265):​n.273+2917A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,970 control chromosomes in the GnomAD database, including 20,672 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 (20672 hom., cov: 32)
• Consequence: ENSG00000257265 ENST00000552098.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.90

Genes affected

ENSG00000257265 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257265	ENST00000552098.1	n.273+2917A>C		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77853 AN: 151852 Hom.: 20659 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.513 AC: 77898 AN: 151970 Hom.: 20672 Cov.: 32 AF XY: 0.508 AC XY: 37749 AN XY: 74284

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.462

Alfa AF: 0.447 Hom.: 2259

Bravo AF: 0.494

Asia WGS AF: 0.316 AC: 1106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.84
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7132840; hg19: chr12-71411561;