chr2-169366666-C-G

Variant names:

• chr2-169366666-C-G
• rs700552

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 0.584 in 152,072 control chromosomes in the GnomAD database, including 26,490 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 0.58 (26490 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.641 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: 0.585 AC: 88837 AN: 151954 Hom.: 26476 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.584 AC: 88884 AN: 152072 Hom.: 26490 Cov.: 32 AF XY: 0.581 AC XY: 43170 AN XY: 74348

African (AFR) AF: 0.490 AC: 20299 AN: 41462

American (AMR) AF: 0.619 AC: 9459 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2332 AN: 3472

East Asian (EAS) AF: 0.308 AC: 1592 AN: 5168

South Asian (SAS) AF: 0.560 AC: 2700 AN: 4818

European-Finnish (FIN) AF: 0.626 AC: 6618 AN: 10572

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.646 AC: 43931 AN: 67992

Other (OTH) AF: 0.588 AC: 1240 AN: 2108

Alfa AF: 0.624 Hom.: 16746

Bravo AF: 0.579

Asia WGS AF: 0.445 AC: 1549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.65
PhyloP100		0.026

Splicing

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

Other links and lift over

dbSNP: rs700552; hg19: chr2-170223176;