rs2662296

Variant names:

• chr5-121747112-C-G
• rs2662296

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 0.241 in 152,028 control chromosomes in the GnomAD database, including 5,940 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 0.24 (5940 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36619 AN: 151908 Hom.: 5915 Cov.: 32

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.241 AC: 36688 AN: 152028 Hom.: 5940 Cov.: 32 AF XY: 0.241 AC XY: 17880 AN XY: 74284

African (AFR) AF: 0.463 AC: 19192 AN: 41452

American (AMR) AF: 0.230 AC: 3506 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3468

East Asian (EAS) AF: 0.207 AC: 1069 AN: 5166

South Asian (SAS) AF: 0.189 AC: 911 AN: 4822

European-Finnish (FIN) AF: 0.173 AC: 1822 AN: 10546

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9088 AN: 67988

Other (OTH) AF: 0.225 AC: 473 AN: 2106

Alfa AF: 0.191 Hom.: 497

Bravo AF: 0.258

Asia WGS AF: 0.214 AC: 743 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.44
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs2662296; hg19: chr5-121082807;