chr11-60862923-C-T

Variant names:

• chr11-60862923-C-T
• rs679682

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.228 in 152,058 control chromosomes in the GnomAD database, including 5,231 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 0.23 (5231 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34733 AN: 151940 Hom.: 5236 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.228 AC: 34745 AN: 152058 Hom.: 5231 Cov.: 32 AF XY: 0.239 AC XY: 17769 AN XY: 74324

African (AFR) AF: 0.101 AC: 4208 AN: 41504

American (AMR) AF: 0.283 AC: 4329 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 394 AN: 3470

East Asian (EAS) AF: 0.738 AC: 3810 AN: 5164

South Asian (SAS) AF: 0.390 AC: 1881 AN: 4828

European-Finnish (FIN) AF: 0.329 AC: 3465 AN: 10530

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 16002 AN: 67970

Other (OTH) AF: 0.202 AC: 425 AN: 2106

Alfa AF: 0.221 Hom.: 5074

Bravo AF: 0.221

Asia WGS AF: 0.493 AC: 1711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.98
DANN	Benign	0.79
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs679682; hg19: chr11-60630396;