11-61975806-T-C

Variant names:

• chr11-61975806-T-C
• rs17156616

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;