rs3824304

chr8-6926753-C-T

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 0.0716 in 152,224 control chromosomes in the GnomAD database, including 555 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 0.072 (555 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.213 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: 0.0717 AC: 10899 AN: 152106 Hom.: 555 Cov.: 33

Gnomad AFR AF: 0.0285

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0874

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.0871

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0627

Gnomad OTH AF: 0.0649

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

GnomAD4 genome AF: 0.0716 AC: 10905 AN: 152224 Hom.: 555 Cov.: 33 AF XY: 0.0782 AC XY: 5821 AN XY: 74426

Gnomad4 AFR AF: 0.0286

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.0874

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.0869

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0627

Gnomad4 OTH AF: 0.0633

Alfa AF: 0.0699 Hom.: 88

Bravo AF: 0.0712

Asia WGS AF: 0.153 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.36
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3824304; hg19: chr8-6784275;