11-65960328-T-C

Variant names:

• chr11-65960328-T-C
• rs593525

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 0.502 in 151,446 control chromosomes in the GnomAD database, including 19,364 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 0.50 (19364 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.97
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.502 AC: 75923 AN: 151336 Hom.: 19343 Cov.: 30

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.502 AC: 75989 AN: 151446 Hom.: 19364 Cov.: 30 AF XY: 0.502 AC XY: 37123 AN XY: 73968

African (AFR) AF: 0.511 AC: 21063 AN: 41232

American (AMR) AF: 0.607 AC: 9241 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1707 AN: 3466

East Asian (EAS) AF: 0.678 AC: 3501 AN: 5162

South Asian (SAS) AF: 0.453 AC: 2172 AN: 4800

European-Finnish (FIN) AF: 0.415 AC: 4328 AN: 10432

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.476 AC: 32325 AN: 67844

Other (OTH) AF: 0.504 AC: 1055 AN: 2092

Alfa AF: 0.487 Hom.: 34847

Bravo AF: 0.522

Asia WGS AF: 0.567 AC: 1969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.61
DANN	Benign	0.38
PhyloP100		-5.0

Splicing

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

Other links and lift over

dbSNP: rs593525; hg19: chr11-65727799;