rs4088472

Variant names:

• chr11-63412012-G-A
• rs4088472

Your query was ambiguous. Multiple possible variants found:

• chr11-63412012-G-A
• chr11-63412012-G-C
• chr11-63412012-G-T

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 0.37 in 150,948 control chromosomes in the GnomAD database, including 11,835 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 0.37 (11835 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 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: 0.369 AC: 55701 AN: 150846 Hom.: 11811 Cov.: 31

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.221

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.370 AC: 55779 AN: 150948 Hom.: 11835 Cov.: 31 AF XY: 0.374 AC XY: 27554 AN XY: 73696

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.384

Alfa AF: 0.304 Hom.: 1012

Bravo AF: 0.389

Asia WGS AF: 0.638 AC: 2209 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4088472; hg19: chr11-63179484;