2-83677488-A-G

Variant names:

• chr2-83677488-A-G
• rs1551194

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 0.949 in 152,152 control chromosomes in the GnomAD database, including 68,737 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 0.95 (68737 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.972 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: 0.949 AC: 144349 AN: 152034 Hom.: 68687 Cov.: 32

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.977

Gnomad AMR AF: 0.975

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.979

Gnomad OTH AF: 0.958

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

GnomAD4 genome AF: 0.949 AC: 144455 AN: 152152 Hom.: 68737 Cov.: 32 AF XY: 0.947 AC XY: 70412 AN XY: 74364

African (AFR) AF: 0.899 AC: 37320 AN: 41526

American (AMR) AF: 0.975 AC: 14893 AN: 15278

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3469 AN: 3470

East Asian (EAS) AF: 0.922 AC: 4747 AN: 5150

South Asian (SAS) AF: 0.837 AC: 4031 AN: 4818

European-Finnish (FIN) AF: 0.967 AC: 10263 AN: 10608

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.979 AC: 66538 AN: 67984

Other (OTH) AF: 0.954 AC: 2015 AN: 2112

Alfa AF: 0.944 Hom.: 25608

Bravo AF: 0.951

Asia WGS AF: 0.866 AC: 3014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.048
DANN	Benign	0.54
PhyloP100		-1.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1551194;

hg19: chr2-83904612;