rs7953959

Positions:

• chr12-97134362-C-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, non coding transcript 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: ENST00000552238.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000552238.1	n.40-50714C>T		intron_variant, non_coding_transcript_variant		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;