rs2324753

Variant names:

• chr6-84848744-G-A
• rs2324753

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 0.371 in 152,056 control chromosomes in the GnomAD database, including 12,200 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 0.37 (12200 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.815

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.57 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: 0.371 AC: 56367 AN: 151938 Hom.: 12196 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.371 AC: 56390 AN: 152056 Hom.: 12200 Cov.: 33 AF XY: 0.374 AC XY: 27761 AN XY: 74298

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.402

Alfa AF: 0.443 Hom.: 7722

Bravo AF: 0.346

Asia WGS AF: 0.483 AC: 1675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	12
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2324753; hg19: chr6-85558462;