2-224078968-G-A

Variant names:

• chr2-224078968-G-A
• rs6740660

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 0.158 in 152,234 control chromosomes in the GnomAD database, including 1,999 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 0.16 (1999 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.193 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: 0.158 AC: 24082 AN: 152116 Hom.: 1998 Cov.: 33

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.158 AC: 24090 AN: 152234 Hom.: 1999 Cov.: 33 AF XY: 0.158 AC XY: 11795 AN XY: 74450

African (AFR) AF: 0.196 AC: 8149 AN: 41518

American (AMR) AF: 0.167 AC: 2561 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 619 AN: 3470

East Asian (EAS) AF: 0.158 AC: 820 AN: 5182

South Asian (SAS) AF: 0.131 AC: 633 AN: 4824

European-Finnish (FIN) AF: 0.112 AC: 1188 AN: 10612

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9709 AN: 68014

Other (OTH) AF: 0.135 AC: 285 AN: 2116

Alfa AF: 0.149 Hom.: 7741

Bravo AF: 0.162

Asia WGS AF: 0.127 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.3
DANN	Benign	0.80
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs6740660; hg19: chr2-224943685;