rs11242909

Positions:

• chr6-477065-C-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: ENST00000661640.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661640.1	n.2193C>T		non_coding_transcript_exon_variant	2/2

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;