chr11-124848069-T-C

Variant names:

• chr11-124848069-T-C
• rs1940177

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 0.24 in 152,044 control chromosomes in the GnomAD database, including 4,912 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 (4912 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 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: 0.240 AC: 36484 AN: 151928 Hom.: 4893 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.240 AC: 36557 AN: 152044 Hom.: 4912 Cov.: 32 AF XY: 0.244 AC XY: 18117 AN XY: 74328

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.210

Alfa AF: 0.230 Hom.: 675

Bravo AF: 0.254

Asia WGS AF: 0.239 AC: 834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.6
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1940177; hg19: chr11-124717965;