rs146250

Variant names:

• chr6-142567378-G-A
• rs146250
• ENST00000447311.1:n.178-22385C>T

Variant summary

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

The ENST00000447311.1(ENSG00000236366):​n.178-22385C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.098 in 152,062 control chromosomes in the GnomAD database, including 841 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 0.098 (841 hom., cov: 32)
• Consequence: ENSG00000236366 ENST00000447311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 3 publications found

Genes affected

ENSG00000236366 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447311.1. 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
	LOC153910	NR_027311.1		n.361+28922C>T		intron	N/A
	LOC153910	NR_027312.1		n.178-22385C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000236366	ENST00000447311.1	TSL:2	n.178-22385C>T		intron	N/A
	ENSG00000236366	ENST00000635073.1	TSL:4	n.301-22385C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0980 AC: 14897 AN: 151944 Hom.: 842 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.0679

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0276

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0918

Gnomad OTH AF: 0.0867

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

GnomAD4 genome AF: 0.0980 AC: 14907 AN: 152062 Hom.: 841 Cov.: 32 AF XY: 0.0983 AC XY: 7307 AN XY: 74328

African (AFR) AF: 0.134 AC: 5547 AN: 41424

American (AMR) AF: 0.0678 AC: 1037 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0937 AC: 325 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5180

South Asian (SAS) AF: 0.0278 AC: 134 AN: 4814

European-Finnish (FIN) AF: 0.127 AC: 1345 AN: 10582

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0918 AC: 6239 AN: 67994

Other (OTH) AF: 0.0853 AC: 180 AN: 2110

Alfa AF: 0.0900 Hom.: 1627

Bravo AF: 0.0946

Asia WGS AF: 0.0270 AC: 92 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.79
PhyloP100		-0.48
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs146250; hg19: chr6-142888515;