rs4298928

Variant names:

• chr11-81759372-A-G
• rs4298928

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 151,304 control chromosomes in the GnomAD database, including 15,742 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 (15742 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.6 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: 68906 AN: 151186 Hom.: 15740 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.456 AC: 68927 AN: 151304 Hom.: 15742 Cov.: 32 AF XY: 0.457 AC XY: 33771 AN XY: 73946

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.619

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.440

Alfa AF: 0.479 Hom.: 7534

Bravo AF: 0.445

Asia WGS AF: 0.538 AC: 1867 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.5
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: rs4298928; hg19: chr11-81470414;