rs680930

Variant names:

• chr3-22985397-A-C
• rs680930

Your query was ambiguous. Multiple possible variants found:

• chr3-22985397-A-C
• chr3-22985397-A-G
• chr3-22985397-A-T

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 0.6 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.597 AC: 24718 AN: 41384

American (AMR) AF: 0.637 AC: 9730 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2363 AN: 3470

East Asian (EAS) AF: 0.439 AC: 2259 AN: 5148

South Asian (SAS) AF: 0.644 AC: 3095 AN: 4808

European-Finnish (FIN) AF: 0.545 AC: 5734 AN: 10530

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41359 AN: 67956

Other (OTH) AF: 0.604 AC: 1276 AN: 2112

Alfa AF: 0.607 Hom.: 116638

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
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs680930; hg19: chr3-23026888;