11-123777625-T-G

Variant names:

• chr11-123777625-T-G
• rs17744026

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.250

Alfa AF: 0.289 Hom.: 8722

Bravo AF: 0.234

Asia WGS AF: 0.137 AC: 479 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17744026; hg19: chr11-123648333;