chr6-146026266-A-G

Variant names:

• chr6-146026266-A-G
• rs863820
• ENST00000766423.1:n.1889T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000766423.1(ENSG00000299793):​n.1889T>C 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 0.391 in 152,040 control chromosomes in the GnomAD database, including 11,964 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 0.39 (11964 hom., cov: 32)
• Consequence: ENSG00000299793 ENST00000766423.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 6 publications found

Genes affected

ENSG00000299793 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 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
ENSG00000299793	ENST00000766423.1	n.1889T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59395 AN: 151922 Hom.: 11951 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.391 AC: 59430 AN: 152040 Hom.: 11964 Cov.: 32 AF XY: 0.393 AC XY: 29211 AN XY: 74336

African (AFR) AF: 0.322 AC: 13354 AN: 41460

American (AMR) AF: 0.312 AC: 4771 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1441 AN: 3468

East Asian (EAS) AF: 0.283 AC: 1465 AN: 5168

South Asian (SAS) AF: 0.490 AC: 2360 AN: 4814

European-Finnish (FIN) AF: 0.474 AC: 5007 AN: 10572

Middle Eastern (MID) AF: 0.507 AC: 147 AN: 290

European-Non Finnish (NFE) AF: 0.435 AC: 29595 AN: 67962

Other (OTH) AF: 0.407 AC: 860 AN: 2114

Alfa AF: 0.387 Hom.: 2045

Bravo AF: 0.375

Asia WGS AF: 0.409 AC: 1422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.41
DANN	Benign	0.69
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs863820; hg19: chr6-146347402;