2-56682617-G-C

Variant names:

• chr2-56682617-G-C
• rs6732705

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 0.63 in 152,028 control chromosomes in the GnomAD database, including 31,358 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 0.63 (31358 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 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: 0.630 AC: 95689 AN: 151910 Hom.: 31302 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.630 AC: 95803 AN: 152028 Hom.: 31358 Cov.: 31 AF XY: 0.635 AC XY: 47167 AN XY: 74306

African (AFR) AF: 0.819 AC: 33998 AN: 41506

American (AMR) AF: 0.614 AC: 9379 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1620 AN: 3466

East Asian (EAS) AF: 0.676 AC: 3479 AN: 5150

South Asian (SAS) AF: 0.516 AC: 2490 AN: 4826

European-Finnish (FIN) AF: 0.648 AC: 6845 AN: 10562

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36330 AN: 67930

Other (OTH) AF: 0.598 AC: 1261 AN: 2110

Alfa AF: 0.449 Hom.: 1154

Bravo AF: 0.638

Asia WGS AF: 0.607 AC: 2109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.39
DANN	Benign	0.54
PhyloP100		-1.4

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: rs6732705;

hg19: chr2-56909752;