chr11-24070856-T-C

Position:

• chr11-24070856-T-C

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 0.0558 in 152,232 control chromosomes in the GnomAD database, including 615 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 0.056 (615 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

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 (AMR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0558 AC: 8490 AN: 152114 Hom.: 612 Cov.: 32

Gnomad AFR AF: 0.0123

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0806

Gnomad FIN AF: 0.0206

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0563

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0558 AC: 8497 AN: 152232 Hom.: 615 Cov.: 32 AF XY: 0.0576 AC XY: 4288 AN XY: 74418

Gnomad4 AFR AF: 0.0123

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.0141

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0804

Gnomad4 FIN AF: 0.0206

Gnomad4 NFE AF: 0.0563

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0573 Hom.: 88

Bravo AF: 0.0701

Asia WGS AF: 0.0420 AC: 151 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	1.6
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2176793; hg19: chr11-24092402;