chr6-24399452-G-A

Variant names:

• chr6-24399452-G-A
• rs12523750

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 0.242 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
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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

African (AFR) AF: 0.153 AC: 6327 AN: 41458

American (AMR) AF: 0.258 AC: 3937 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 753 AN: 3468

East Asian (EAS) AF: 0.306 AC: 1575 AN: 5154

South Asian (SAS) AF: 0.348 AC: 1672 AN: 4810

European-Finnish (FIN) AF: 0.397 AC: 4168 AN: 10510

Middle Eastern (MID) AF: 0.202 AC: 59 AN: 292

European-Non Finnish (NFE) AF: 0.259 AC: 17623 AN: 67948

Other (OTH) AF: 0.240 AC: 503 AN: 2096

Alfa AF: 0.246 Hom.: 12946

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
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs12523750; hg19: chr6-24399680;