rs11128275

Variant names:

• chr3-72466809-G-A
• rs11128275

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 0.456 in 152,006 control chromosomes in the GnomAD database, including 17,548 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 0.46 (17548 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 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: 0.456 AC: 69225 AN: 151888 Hom.: 17534 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.456 AC: 69253 AN: 152006 Hom.: 17548 Cov.: 32 AF XY: 0.465 AC XY: 34554 AN XY: 74280

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.461

Alfa AF: 0.508 Hom.: 16197

Bravo AF: 0.447

Asia WGS AF: 0.591 AC: 2054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.24
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11128275; hg19: chr3-72515960;