2-614168-A-G

Variant names:

• chr2-614168-A-G
• rs2947411

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 0.816 in 152,092 control chromosomes in the GnomAD database, including 50,719 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 0.82 (50719 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 54 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.816 AC: 123981 AN: 151972 Hom.: 50696 Cov.: 31

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.792

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.816 AC: 124055 AN: 152092 Hom.: 50719 Cov.: 31 AF XY: 0.819 AC XY: 60858 AN XY: 74334

African (AFR) AF: 0.774 AC: 32075 AN: 41452

American (AMR) AF: 0.853 AC: 13046 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2566 AN: 3470

East Asian (EAS) AF: 0.920 AC: 4751 AN: 5162

South Asian (SAS) AF: 0.798 AC: 3849 AN: 4822

European-Finnish (FIN) AF: 0.847 AC: 8975 AN: 10590

Middle Eastern (MID) AF: 0.779 AC: 226 AN: 290

European-Non Finnish (NFE) AF: 0.825 AC: 56099 AN: 67992

Other (OTH) AF: 0.813 AC: 1721 AN: 2116

Alfa AF: 0.822 Hom.: 156795

Bravo AF: 0.815

Asia WGS AF: 0.858 AC: 2985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.52
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2947411; hg19: chr2-614168;