rs55917927

chr12-34098211-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0272 in 152,336 control chromosomes in the GnomAD database, including 68 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 0.027 (68 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0272 (4144/152336) while in subpopulation NFE AF= 0.0456 (3102/68024). AF 95% confidence interval is 0.0443. There are 68 homozygotes in gnomad4. There are 1890 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 68 gene

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: 0.0272 AC: 4143 AN: 152218 Hom.: 68 Cov.: 32

Gnomad AFR AF: 0.00832

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0223

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00394

Gnomad FIN AF: 0.0228

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0456

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0272 AC: 4144 AN: 152336 Hom.: 68 Cov.: 32 AF XY: 0.0254 AC XY: 1890 AN XY: 74500

Gnomad4 AFR AF: 0.00830

Gnomad4 AMR AF: 0.0223

Gnomad4 ASJ AF: 0.00749

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00394

Gnomad4 FIN AF: 0.0228

Gnomad4 NFE AF: 0.0456

Gnomad4 OTH AF: 0.0241

Alfa AF: 0.0374 Hom.: 14

Bravo AF: 0.0261

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	4.0
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55917927; hg19: chr12-34251146;