chr11-65960328-T-C

Variant names:

• chr11-65960328-T-C
• rs593525

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 0.502 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.502 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

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.504

Alfa AF: 0.480 Hom.: 22185

Bravo AF: 0.522

Asia WGS AF: 0.567 AC: 1969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs593525; hg19: chr11-65727799;