chr11-123777625-T-G

Variant names:

• chr11-123777625-T-G
• rs17744026

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 0.237 in 152,138 control chromosomes in the GnomAD database, including 4,748 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 0.24 (4748 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36092 AN: 152020 Hom.: 4749 Cov.: 33

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.237 AC: 36092 AN: 152138 Hom.: 4748 Cov.: 33 AF XY: 0.233 AC XY: 17323 AN XY: 74378

African (AFR) AF: 0.148 AC: 6121 AN: 41494

American (AMR) AF: 0.241 AC: 3684 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 818 AN: 3468

East Asian (EAS) AF: 0.103 AC: 535 AN: 5186

South Asian (SAS) AF: 0.170 AC: 819 AN: 4826

European-Finnish (FIN) AF: 0.268 AC: 2835 AN: 10584

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.302 AC: 20501 AN: 67976

Other (OTH) AF: 0.250 AC: 529 AN: 2114

Alfa AF: 0.285 Hom.: 10719

Bravo AF: 0.234

Asia WGS AF: 0.137 AC: 479 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.4
DANN	Benign	0.59
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs17744026; hg19: chr11-123648333;