11-18264227-A-T

Variant names:

• chr11-18264227-A-T
• rs4638289

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 0.668 in 152,066 control chromosomes in the GnomAD database, including 34,216 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 0.67 (34216 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

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 (NFE) allele frequency at 95% confidence interval = 0.688 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: 0.668 AC: 101503 AN: 151948 Hom.: 34178 Cov.: 32

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.668 AC: 101593 AN: 152066 Hom.: 34216 Cov.: 32 AF XY: 0.668 AC XY: 49638 AN XY: 74336

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.603

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.682

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.610

Alfa AF: 0.514 Hom.: 807

Bravo AF: 0.656

Asia WGS AF: 0.701 AC: 2436 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	0.057
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4638289; hg19: chr11-18285774;