11-61975806-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 0.15 in 152,212 control chromosomes in the GnomAD database, including 2,683 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 0.15 (2683 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 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: 0.150 AC: 22786 AN: 152094 Hom.: 2677 Cov.: 33

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0832

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.150 AC: 22809 AN: 152212 Hom.: 2683 Cov.: 33 AF XY: 0.157 AC XY: 11710 AN XY: 74414

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.0832

Gnomad4 OTH AF: 0.126

Alfa AF: 0.119 Hom.: 179

Bravo AF: 0.159

Asia WGS AF: 0.324 AC: 1126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
Cadd	Benign	13
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17156616; hg19: chr11-61743278;