ENST00000650727.1:n.3037-1028A>C

Variant names:

• chr6-126498553-T-G
• rs4418209
• ENST00000650727.1:n.3037-1028A>C

Variant summary

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

The ENST00000650727.1(ENSG00000293110):​n.3037-1028A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 151,816 control chromosomes in the GnomAD database, including 16,454 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 0.43 (16454 hom., cov: 31)
• Consequence: ENSG00000293110 ENST00000650727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.729
• Publications: 26 publications found

Genes affected

ENSG00000293110 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 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
ENSG00000293110	ENST00000650727.1	n.3037-1028A>C		intron_variant	Intron 14 of 14
ENSG00000293110	ENST00000651326.1	n.2290-25959A>C		intron_variant	Intron 5 of 6
ENSG00000293110	ENST00000652383.1	n.630+33110A>C		intron_variant	Intron 3 of 4
ENSG00000293110	ENST00000652545.1	n.3347-1028A>C		intron_variant	Intron 15 of 15

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65518 AN: 151698 Hom.: 16453 Cov.: 31

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.432 AC: 65522 AN: 151816 Hom.: 16454 Cov.: 31 AF XY: 0.442 AC XY: 32772 AN XY: 74186

African (AFR) AF: 0.211 AC: 8723 AN: 41436

American (AMR) AF: 0.610 AC: 9292 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1679 AN: 3468

East Asian (EAS) AF: 0.974 AC: 5024 AN: 5156

South Asian (SAS) AF: 0.676 AC: 3248 AN: 4806

European-Finnish (FIN) AF: 0.437 AC: 4589 AN: 10506

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31366 AN: 67896

Other (OTH) AF: 0.465 AC: 978 AN: 2104

Alfa AF: 0.421 Hom.: 4626

Bravo AF: 0.438

Asia WGS AF: 0.692 AC: 2402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.68
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs4418209; hg19: chr6-126819699; COSMIC: COSV69424779;