rs12155672

chr8-127494779-A-Gchr8-127494779-A-T

Variant summary

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

The variant allele was found at a frequency of 0.473 in 148,588 control chromosomes in the GnomAD database, including 16,754 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 0.47 (16754 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.473 AC: 70268 AN: 148470 Hom.: 16748 Cov.: 24

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.473 AC: 70303 AN: 148588 Hom.: 16754 Cov.: 24 AF XY: 0.467 AC XY: 33761 AN XY: 72278

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.457

Alfa AF: 0.482 Hom.: 5549

Bravo AF: 0.471

Asia WGS AF: 0.403 AC: 1406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.4
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12155672; hg19: chr8-128507024; COSMIC: COSV68250257;