rs146250

Positions:

• chr6-142567378-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000236366 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC153910	NR_027311.1	n.361+28922C>T		intron_variant
LOC153910	NR_027312.1	n.178-22385C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000236366	ENST00000447311.1	n.178-22385C>T		intron_variant		2
ENSG00000236366	ENST00000635073.1	n.301-22385C>T		intron_variant		4

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

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.0678

Gnomad4 ASJ AF: 0.0937

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0278

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.0918

Gnomad4 OTH AF: 0.0853

Alfa AF: 0.0861 Hom.: 918

Bravo AF: 0.0946

Asia WGS AF: 0.0270 AC: 92 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs146250; hg19: chr6-142888515;