rs4298928

Positions:

• chr11-81759372-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;