rs7954855

Positions:

• chr12-6125857-T-C

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 0.532 in 151,764 control chromosomes in the GnomAD database, including 22,455 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 (22455 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.636 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: 0.532 AC: 80676 AN: 151648 Hom.: 22455 Cov.: 31

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.532 AC: 80691 AN: 151764 Hom.: 22455 Cov.: 31 AF XY: 0.526 AC XY: 39018 AN XY: 74136

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.641

Gnomad4 OTH AF: 0.529

Alfa AF: 0.583 Hom.: 3297

Bravo AF: 0.516

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.23
DANN	Benign	0.043

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7954855; hg19: chr12-6235023;