rs11242909

Variant names:

• chr6-477065-C-T
• rs11242909
• ENST00000661640.1:n.2193C>T

Variant summary

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

The ENST00000661640.1(ENSG00000286364):​n.2193C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 152,100 control chromosomes in the GnomAD database, including 35,558 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 0.68 (35558 hom., cov: 33)
• Consequence: ENSG00000286364 ENST00000661640.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09

Genes affected

ENSG00000286364 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.747 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
ENSG00000286364	ENST00000661640.1	n.2193C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102911 AN: 151982 Hom.: 35548 Cov.: 33

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.677 AC: 102955 AN: 152100 Hom.: 35558 Cov.: 33 AF XY: 0.673 AC XY: 50073 AN XY: 74354

Gnomad4 AFR AF: 0.588

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.777

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.688

Alfa AF: 0.720 Hom.: 18256

Bravo AF: 0.659

Asia WGS AF: 0.516 AC: 1798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.31
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11242909; hg19: chr6-477065; COSMIC: COSV70615743;