12-71017781-T-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

Genes affected

ENSG00000257265 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.559 AC: 23157 AN: 41428

American (AMR) AF: 0.385 AC: 5871 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1346 AN: 3464

East Asian (EAS) AF: 0.167 AC: 863 AN: 5170

South Asian (SAS) AF: 0.508 AC: 2444 AN: 4814

European-Finnish (FIN) AF: 0.578 AC: 6102 AN: 10564

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.538 AC: 36591 AN: 67950

Other (OTH) AF: 0.462 AC: 975 AN: 2112

Alfa AF: 0.450 Hom.: 2371

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
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs7132840; hg19: chr12-71411561;