rs898309

Variant names:

• chr11-112754370-A-G
• rs898309
• ENST00000688876.1:n.585-6810A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000688876.1(ENSG00000285769):​n.585-6810A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 151,996 control chromosomes in the GnomAD database, including 32,876 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 0.64 (32876 hom., cov: 32)
• Consequence: ENSG00000285769 ENST00000688876.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

Genes affected

ENSG00000285769 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.761 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
ENSG00000285769	ENST00000688876.1	n.585-6810A>G		intron_variant	Intron 3 of 3
ENSG00000285769	ENST00000691666.1	n.690-6810A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97394 AN: 151876 Hom.: 32859 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.796

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.641 AC: 97464 AN: 151996 Hom.: 32876 Cov.: 32 AF XY: 0.636 AC XY: 47259 AN XY: 74294

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.746

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.766

Gnomad4 OTH AF: 0.681

Alfa AF: 0.728 Hom.: 18670

Bravo AF: 0.635

Asia WGS AF: 0.543 AC: 1892 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	0.56
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: rs898309; hg19: chr11-112625093;