chr6-477065-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

ENSG00000286364 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661640.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286364	ENST00000661640.1		n.2193C>T		non_coding_transcript_exon	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

African (AFR) AF: 0.588 AC: 24379 AN: 41464

American (AMR) AF: 0.605 AC: 9248 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2379 AN: 3470

East Asian (EAS) AF: 0.501 AC: 2592 AN: 5174

South Asian (SAS) AF: 0.542 AC: 2611 AN: 4818

European-Finnish (FIN) AF: 0.777 AC: 8208 AN: 10570

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.753 AC: 51174 AN: 68002

Other (OTH) AF: 0.688 AC: 1452 AN: 2112

Alfa AF: 0.722 Hom.: 20357

Bravo AF: 0.659

Asia WGS AF: 0.516 AC: 1798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.31
DANN	Benign	0.31
PhyloP100		-2.1

Splicing

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

Other links and lift over

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