rs9681213

Variant names:

• chr3-25220-G-A
• rs9681213

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 0.277 in 152,014 control chromosomes in the GnomAD database, including 6,201 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 0.28 (6201 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.347 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: 0.277 AC: 42045 AN: 151896 Hom.: 6197 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.0667

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.277 AC: 42080 AN: 152014 Hom.: 6201 Cov.: 32 AF XY: 0.276 AC XY: 20519 AN XY: 74320

African (AFR) AF: 0.226 AC: 9349 AN: 41450

American (AMR) AF: 0.228 AC: 3487 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1248 AN: 3466

East Asian (EAS) AF: 0.0666 AC: 345 AN: 5178

South Asian (SAS) AF: 0.361 AC: 1738 AN: 4810

European-Finnish (FIN) AF: 0.266 AC: 2807 AN: 10550

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22044 AN: 67974

Other (OTH) AF: 0.278 AC: 583 AN: 2100

Alfa AF: 0.311 Hom.: 17847

Bravo AF: 0.270

Asia WGS AF: 0.228 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.43
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs9681213; hg19: chr3-66894;