11-64544425-T-G

Variant names:

• chr11-64544425-T-G
• rs4930423

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 0.315 in 152,196 control chromosomes in the GnomAD database, including 9,569 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 0.32 (9569 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 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: 0.315 AC: 47953 AN: 152078 Hom.: 9574 Cov.: 32

Gnomad AFR AF: 0.0994

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.0196

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.315 AC: 47945 AN: 152196 Hom.: 9569 Cov.: 32 AF XY: 0.311 AC XY: 23147 AN XY: 74400

African (AFR) AF: 0.0993 AC: 4127 AN: 41554

American (AMR) AF: 0.276 AC: 4213 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1519 AN: 3472

East Asian (EAS) AF: 0.0196 AC: 102 AN: 5192

South Asian (SAS) AF: 0.320 AC: 1539 AN: 4816

European-Finnish (FIN) AF: 0.396 AC: 4187 AN: 10578

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30904 AN: 67984

Other (OTH) AF: 0.328 AC: 692 AN: 2112

Alfa AF: 0.222 Hom.: 583

Bravo AF: 0.296

Asia WGS AF: 0.147 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.76
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs4930423; hg19: chr11-64311897;