rs12523750

Variant names:

• chr6-24399452-G-A
• rs12523750

Your query was ambiguous. Multiple possible variants found:

• chr6-24399452-G-A
• chr6-24399452-G-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 0.242 in 151,908 control chromosomes in the GnomAD database, including 4,783 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 0.24 (4783 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.334 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: 0.242 AC: 36689 AN: 151794 Hom.: 4776 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.242 AC: 36711 AN: 151908 Hom.: 4783 Cov.: 32 AF XY: 0.250 AC XY: 18577 AN XY: 74242

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.240

Alfa AF: 0.243 Hom.: 4184

Bravo AF: 0.223

Asia WGS AF: 0.340 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.87
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12523750; hg19: chr6-24399680;