11-61026179-C-G

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 0.393 in 151,892 control chromosomes in the GnomAD database, including 12,070 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 0.39 (12070 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59593 AN: 151774 Hom.: 12049 Cov.: 31

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.393 AC: 59644 AN: 151892 Hom.: 12070 Cov.: 31 AF XY: 0.387 AC XY: 28762 AN XY: 74236

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.429

Alfa AF: 0.399 Hom.: 6855

Bravo AF: 0.402

Asia WGS AF: 0.348 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.47
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4939490; hg19: chr11-60793651;