3-122181013-C-T

Variant names:

• chr3-122181013-C-T
• rs7648044

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 0.172 in 152,096 control chromosomes in the GnomAD database, including 2,332 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 0.17 (2332 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 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: 0.172 AC: 26158 AN: 151978 Hom.: 2326 Cov.: 31

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.172 AC: 26165 AN: 152096 Hom.: 2332 Cov.: 31 AF XY: 0.168 AC XY: 12466 AN XY: 74346

African (AFR) AF: 0.204 AC: 8455 AN: 41470

American (AMR) AF: 0.109 AC: 1674 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 598 AN: 3472

East Asian (EAS) AF: 0.0307 AC: 159 AN: 5186

South Asian (SAS) AF: 0.150 AC: 721 AN: 4816

European-Finnish (FIN) AF: 0.196 AC: 2073 AN: 10578

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11935 AN: 67968

Other (OTH) AF: 0.164 AC: 345 AN: 2110

Alfa AF: 0.182 Hom.: 318

Bravo AF: 0.167

Asia WGS AF: 0.0840 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.55
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs7648044; hg19: chr3-121899860;