6-150458046-C-T

Variant names:

• chr6-150458046-C-T
• rs4870523
• ENST00000743667.1:n.239-34223C>T

Variant summary

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

The ENST00000743667.1(ENSG00000296927):​n.239-34223C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,032 control chromosomes in the GnomAD database, including 9,556 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 0.35 (9556 hom., cov: 33)
• Consequence: ENSG00000296927 ENST00000743667.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 2 publications found

Genes affected

ENSG00000296927 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000743667.1. 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
	ENSG00000296927	ENST00000743667.1		n.239-34223C>T		intron	N/A
	ENSG00000296927	ENST00000743668.1		n.239-34223C>T		intron	N/A
	ENSG00000296927	ENST00000743669.1		n.203-34223C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53709 AN: 151914 Hom.: 9548 Cov.: 33

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.354 AC: 53761 AN: 152032 Hom.: 9556 Cov.: 33 AF XY: 0.351 AC XY: 26057 AN XY: 74278

African (AFR) AF: 0.353 AC: 14660 AN: 41474

American (AMR) AF: 0.348 AC: 5317 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1629 AN: 3464

East Asian (EAS) AF: 0.296 AC: 1525 AN: 5156

South Asian (SAS) AF: 0.354 AC: 1706 AN: 4818

European-Finnish (FIN) AF: 0.297 AC: 3130 AN: 10548

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24519 AN: 67988

Other (OTH) AF: 0.393 AC: 830 AN: 2114

Alfa AF: 0.363 Hom.: 4748

Bravo AF: 0.357

Asia WGS AF: 0.319 AC: 1107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.6
DANN	Benign	0.50
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs4870523; hg19: chr6-150779182;