chr3-22985397-A-C

Variant names:

• chr3-22985397-A-C
• rs680930

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 0.6 in 151,890 control chromosomes in the GnomAD database, including 27,531 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 0.60 (27531 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.829

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 (SAS) allele frequency at 95% confidence interval = 0.626 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: 0.600 AC: 91038 AN: 151772 Hom.: 27508 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.600 AC: 91104 AN: 151890 Hom.: 27531 Cov.: 32 AF XY: 0.596 AC XY: 44189 AN XY: 74200

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.604

Alfa AF: 0.610 Hom.: 56821

Bravo AF: 0.608

Asia WGS AF: 0.546 AC: 1901 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	0.37
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs680930; hg19: chr3-23026888;