2-180490796-G-C

Variant names:

• chr2-180490796-G-C
• rs11692860

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.26 (3631 hom., cov: 18)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.950
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 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: 0.265 AC: 27978 AN: 105650 Hom.: 3628 Cov.: 18

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.349

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.265 AC: 27992 AN: 105690 Hom.: 3631 Cov.: 18 AF XY: 0.274 AC XY: 13424 AN XY: 49006

African (AFR) AF: 0.431 AC: 12767 AN: 29602

American (AMR) AF: 0.210 AC: 1617 AN: 7690

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 431 AN: 2770

East Asian (EAS) AF: 0.217 AC: 735 AN: 3394

South Asian (SAS) AF: 0.301 AC: 966 AN: 3208

European-Finnish (FIN) AF: 0.247 AC: 1006 AN: 4080

Middle Eastern (MID) AF: 0.340 AC: 55 AN: 162

European-Non Finnish (NFE) AF: 0.189 AC: 9946 AN: 52666

Other (OTH) AF: 0.271 AC: 381 AN: 1406

Alfa AF: 0.0736 Hom.: 89

Bravo AF: 0.216

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	0.54
DANN	Benign	0.36
PhyloP100		-0.95

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: rs11692860;

hg19: chr2-181355523;