rs12510549

chr4-10274843-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.182 in 152,104 control chromosomes in the GnomAD database, including 2,624 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 0.18 (2624 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

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: 0.182 AC: 27609 AN: 151986 Hom.: 2617 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.182 AC: 27626 AN: 152104 Hom.: 2624 Cov.: 32 AF XY: 0.182 AC XY: 13558 AN XY: 74334

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.185

Alfa AF: 0.205 Hom.: 3231

Bravo AF: 0.183

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.6
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12510549; hg19: chr4-10276467;