rs12510549

Variant names:

• chr4-10274843-T-C
• rs12510549

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 0.182 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
• Publications: 22 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.122 AC: 5071 AN: 41530

American (AMR) AF: 0.244 AC: 3732 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 955 AN: 3470

East Asian (EAS) AF: 0.137 AC: 706 AN: 5162

South Asian (SAS) AF: 0.150 AC: 721 AN: 4820

European-Finnish (FIN) AF: 0.198 AC: 2087 AN: 10558

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13772 AN: 67958

Other (OTH) AF: 0.185 AC: 390 AN: 2110

Alfa AF: 0.198 Hom.: 4251

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
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs12510549; hg19: chr4-10276467;