rs12775535

Positions:

• chr10-25629950-C-T

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 0.0288 in 152,262 control chromosomes in the GnomAD database, including 79 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 0.029 (79 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0288 (4391/152262) while in subpopulation AFR AF= 0.0484 (2012/41552). AF 95% confidence interval is 0.0467. There are 79 homozygotes in gnomad4. There are 2065 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 79 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: 0.0288 AC: 4382 AN: 152144 Hom.: 77 Cov.: 32

Gnomad AFR AF: 0.0483

Gnomad AMI AF: 0.0242

Gnomad AMR AF: 0.0240

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00808

Gnomad FIN AF: 0.0123

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0247

Gnomad OTH AF: 0.0315

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

GnomAD4 genome AF: 0.0288 AC: 4391 AN: 152262 Hom.: 79 Cov.: 32 AF XY: 0.0277 AC XY: 2065 AN XY: 74456

Gnomad4 AFR AF: 0.0484

Gnomad4 AMR AF: 0.0239

Gnomad4 ASJ AF: 0.0207

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00809

Gnomad4 FIN AF: 0.0123

Gnomad4 NFE AF: 0.0247

Gnomad4 OTH AF: 0.0312

Alfa AF: 0.0252 Hom.: 95

Bravo AF: 0.0315

Asia WGS AF: 0.00866 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.1
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12775535; hg19: chr10-25918879;