11-18264227-A-T

Variant names:

• chr11-18264227-A-T
• rs4638289

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 0.668 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
• Publications: 37 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 = 0.688 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

African (AFR) AF: 0.653 AC: 27076 AN: 41464

American (AMR) AF: 0.603 AC: 9221 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1796 AN: 3468

East Asian (EAS) AF: 0.682 AC: 3517 AN: 5160

South Asian (SAS) AF: 0.611 AC: 2948 AN: 4822

European-Finnish (FIN) AF: 0.755 AC: 7984 AN: 10576

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47122 AN: 67984

Other (OTH) AF: 0.610 AC: 1284 AN: 2106

Alfa AF: 0.613 Hom.: 2009

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
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs4638289; hg19: chr11-18285774;