chr10-5025949-T-C

Variant names:

• chr10-5025949-T-C
• rs12411321

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 0.154 in 152,150 control chromosomes in the GnomAD database, including 2,241 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 0.15 (2241 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.239 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: 0.154 AC: 23477 AN: 152032 Hom.: 2242 Cov.: 33

Gnomad AFR AF: 0.0571

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.0663

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.154 AC: 23479 AN: 152150 Hom.: 2241 Cov.: 33 AF XY: 0.157 AC XY: 11698 AN XY: 74366

African (AFR) AF: 0.0569 AC: 2363 AN: 41522

American (AMR) AF: 0.246 AC: 3755 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3468

East Asian (EAS) AF: 0.132 AC: 685 AN: 5172

South Asian (SAS) AF: 0.0672 AC: 323 AN: 4806

European-Finnish (FIN) AF: 0.253 AC: 2680 AN: 10582

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12618 AN: 68004

Other (OTH) AF: 0.161 AC: 341 AN: 2112

Alfa AF: 0.162 Hom.: 289

Bravo AF: 0.153

Asia WGS AF: 0.0920 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.6
DANN	Benign	0.72
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs12411321; hg19: chr10-5068141;