chr2-128785193-C-T

Variant names:

• chr2-128785193-C-T
• rs11690256

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 0.269 in 152,040 control chromosomes in the GnomAD database, including 6,156 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 0.27 (6156 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.270 AC: 40968 AN: 151922 Hom.: 6151 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.269 AC: 40973 AN: 152040 Hom.: 6156 Cov.: 32 AF XY: 0.270 AC XY: 20044 AN XY: 74312

African (AFR) AF: 0.164 AC: 6800 AN: 41504

American (AMR) AF: 0.219 AC: 3337 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 857 AN: 3472

East Asian (EAS) AF: 0.119 AC: 612 AN: 5150

South Asian (SAS) AF: 0.240 AC: 1156 AN: 4818

European-Finnish (FIN) AF: 0.355 AC: 3744 AN: 10548

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23602 AN: 67960

Other (OTH) AF: 0.271 AC: 572 AN: 2114

Alfa AF: 0.296 Hom.: 5728

Bravo AF: 0.252

Asia WGS AF: 0.214 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.66
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs11690256; hg19: chr2-129542767;