chr3-122292307-C-T

Variant names:

• chr3-122292307-C-T
• rs10934581

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 0.269 in 151,968 control chromosomes in the GnomAD database, including 6,279 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 0.27 (6279 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40897 AN: 151850 Hom.: 6284 Cov.: 31

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.00386

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.269 AC: 40883 AN: 151968 Hom.: 6279 Cov.: 31 AF XY: 0.267 AC XY: 19799 AN XY: 74250

African (AFR) AF: 0.162 AC: 6722 AN: 41444

American (AMR) AF: 0.222 AC: 3394 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 902 AN: 3468

East Asian (EAS) AF: 0.00387 AC: 20 AN: 5174

South Asian (SAS) AF: 0.209 AC: 1008 AN: 4816

European-Finnish (FIN) AF: 0.376 AC: 3962 AN: 10526

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23875 AN: 67956

Other (OTH) AF: 0.278 AC: 584 AN: 2104

Alfa AF: 0.304 Hom.: 2402

Bravo AF: 0.252

Asia WGS AF: 0.0900 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.76
DANN	Benign	0.49
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10934581; hg19: chr3-122011154;