chr11-64544425-T-G

Variant names:

• chr11-64544425-T-G
• rs4930423

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 0.315 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.315 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

Gnomad4 AFR AF: 0.0993

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.0196

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.328

Alfa AF: 0.229 Hom.: 576

Bravo AF: 0.296

Asia WGS AF: 0.147 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4930423; hg19: chr11-64311897;