chr11-64539585-G-C

Variant names:

• chr11-64539585-G-C
• rs4930420

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 0.305 in 152,198 control chromosomes in the GnomAD database, including 8,997 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 0.30 (8997 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.869
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.437 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: 0.305 AC: 46392 AN: 152080 Hom.: 9003 Cov.: 32

Gnomad AFR AF: 0.0926

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.0196

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.305 AC: 46379 AN: 152198 Hom.: 8997 Cov.: 32 AF XY: 0.300 AC XY: 22356 AN XY: 74418

African (AFR) AF: 0.0924 AC: 3840 AN: 41536

American (AMR) AF: 0.266 AC: 4072 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1490 AN: 3468

East Asian (EAS) AF: 0.0197 AC: 102 AN: 5188

South Asian (SAS) AF: 0.315 AC: 1517 AN: 4816

European-Finnish (FIN) AF: 0.379 AC: 4020 AN: 10596

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.441 AC: 29992 AN: 67982

Other (OTH) AF: 0.326 AC: 688 AN: 2112

Alfa AF: 0.218 Hom.: 550

Bravo AF: 0.286

Asia WGS AF: 0.145 AC: 508 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	0.34
DANN	Benign	0.30
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs4930420; hg19: chr11-64307057;