chr2-223615542-A-G

Variant names:

• chr2-223615542-A-G
• rs966414

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 0.152 in 152,128 control chromosomes in the GnomAD database, including 3,298 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 0.15 (3298 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 6 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 = 0.374 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: 0.152 AC: 23049 AN: 152010 Hom.: 3279 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.0835

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0657

Gnomad FIN AF: 0.0359

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.0581

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.152 AC: 23111 AN: 152128 Hom.: 3298 Cov.: 32 AF XY: 0.149 AC XY: 11081 AN XY: 74388

African (AFR) AF: 0.379 AC: 15703 AN: 41426

American (AMR) AF: 0.0833 AC: 1274 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0986 AC: 342 AN: 3468

East Asian (EAS) AF: 0.134 AC: 692 AN: 5170

South Asian (SAS) AF: 0.0654 AC: 315 AN: 4818

European-Finnish (FIN) AF: 0.0359 AC: 381 AN: 10608

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.0581 AC: 3949 AN: 68026

Other (OTH) AF: 0.124 AC: 261 AN: 2112

Alfa AF: 0.0951 Hom.: 1045

Bravo AF: 0.165

Asia WGS AF: 0.108 AC: 375 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	0.13
DANN	Benign	0.33
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs966414; hg19: chr2-224480259;