rs7953959

Variant names:

• chr12-97134362-C-T
• rs7953959
• ENST00000552238.1:n.40-50714C>T

Variant summary

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

The ENST00000552238.1(ENSG00000258131):​n.40-50714C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,906 control chromosomes in the GnomAD database, including 21,284 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 0.53 (21284 hom., cov: 32)
• Consequence: ENSG00000258131 ENST00000552238.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

Genes affected

ENSG00000258131 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.583 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
ENSG00000258131	ENST00000552238.1	n.40-50714C>T		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79872 AN: 151788 Hom.: 21253 Cov.: 32

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.526 AC: 79952 AN: 151906 Hom.: 21284 Cov.: 32 AF XY: 0.523 AC XY: 38813 AN XY: 74222

Gnomad4 AFR AF: 0.590

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.531

Alfa AF: 0.515 Hom.: 9145

Bravo AF: 0.536

Asia WGS AF: 0.382 AC: 1330 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7953959; hg19: chr12-97528140;