rs7954855

Variant names:

• chr12-6125857-T-C
• rs7954855

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.376 AC: 15574 AN: 41374

American (AMR) AF: 0.477 AC: 7276 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1743 AN: 3468

East Asian (EAS) AF: 0.420 AC: 2145 AN: 5108

South Asian (SAS) AF: 0.463 AC: 2224 AN: 4808

European-Finnish (FIN) AF: 0.603 AC: 6348 AN: 10532

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.641 AC: 43553 AN: 67928

Other (OTH) AF: 0.529 AC: 1111 AN: 2102

Alfa AF: 0.583 Hom.: 3297

Bravo AF: 0.516

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.23
DANN	Benign	0.043
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs7954855; hg19: chr12-6235023;