rs898309

Positions:

• chr11-112754370-A-G

Variant summary

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

The ENST00000691666.1(ENSG00000285769):​n.690-6810A>G variant causes a intron, non coding transcript 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: ENST00000691666.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000691666.1	n.690-6810A>G		intron_variant, non_coding_transcript_variant
	ENST00000688876.1	n.585-6810A>G		intron_variant, non_coding_transcript_variant

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;