3-122153978-C-T

Variant names:

• chr3-122153978-C-T
• rs6438700

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 0.199 in 152,122 control chromosomes in the GnomAD database, including 3,213 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 0.20 (3213 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30200 AN: 152004 Hom.: 3211 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0311

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.199 AC: 30205 AN: 152122 Hom.: 3213 Cov.: 32 AF XY: 0.194 AC XY: 14414 AN XY: 74360

African (AFR) AF: 0.283 AC: 11733 AN: 41470

American (AMR) AF: 0.120 AC: 1837 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 600 AN: 3472

East Asian (EAS) AF: 0.0312 AC: 161 AN: 5166

South Asian (SAS) AF: 0.178 AC: 856 AN: 4820

European-Finnish (FIN) AF: 0.197 AC: 2084 AN: 10596

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.182 AC: 12368 AN: 67990

Other (OTH) AF: 0.180 AC: 380 AN: 2110

Alfa AF: 0.162 Hom.: 1167

Bravo AF: 0.196

Asia WGS AF: 0.0970 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.72
DANN	Benign	0.24
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs6438700; hg19: chr3-121872825;