rs12256830

Variant names:

• chr10-53624983-C-T
• rs12256830

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 0.0539 in 152,026 control chromosomes in the GnomAD database, including 395 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 0.054 (395 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0537 AC: 8158 AN: 151910 Hom.: 389 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0375

Gnomad ASJ AF: 0.0495

Gnomad EAS AF: 0.0506

Gnomad SAS AF: 0.0517

Gnomad FIN AF: 0.0190

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0258

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0539 AC: 8198 AN: 152026 Hom.: 395 Cov.: 32 AF XY: 0.0528 AC XY: 3927 AN XY: 74316

African (AFR) AF: 0.118 AC: 4876 AN: 41414

American (AMR) AF: 0.0376 AC: 573 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0495 AC: 172 AN: 3472

East Asian (EAS) AF: 0.0503 AC: 260 AN: 5164

South Asian (SAS) AF: 0.0520 AC: 251 AN: 4828

European-Finnish (FIN) AF: 0.0190 AC: 202 AN: 10606

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0258 AC: 1757 AN: 67984

Other (OTH) AF: 0.0398 AC: 84 AN: 2108

Alfa AF: 0.0359 Hom.: 689

Bravo AF: 0.0588

Asia WGS AF: 0.0460 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.063
DANN	Benign	0.66
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs12256830; hg19: chr10-55384743;