22-46143831-C-T

Variant names:

• chr22-46143831-C-T
• rs135559
• ENST00000846781.1:n.975C>T

Variant summary

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

The ENST00000846781.1(ENSG00000310052):​n.975C>T 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 0.996 in 152,372 control chromosomes in the GnomAD database, including 75,508 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 1.0 (75508 hom., cov: 35)
• Consequence: ENSG00000310052 ENST00000846781.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233
• Publications: 1 publications found

Genes affected

ENSG00000310052 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846781.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310052	ENST00000846781.1		n.975C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000310052	ENST00000846782.1		n.939C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000310052	ENST00000846783.1		n.777C>T		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.996 AC: 151573 AN: 152254 Hom.: 75449 Cov.: 35

Gnomad AFR AF: 0.999

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.996

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 0.974

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.997

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

GnomAD4 genome AF: 0.996 AC: 151691 AN: 152372 Hom.: 75508 Cov.: 35 AF XY: 0.995 AC XY: 74103 AN XY: 74504

African (AFR) AF: 0.999 AC: 41555 AN: 41580

American (AMR) AF: 0.996 AC: 15244 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 3470 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5190 AN: 5190

South Asian (SAS) AF: 1.00 AC: 4829 AN: 4830

European-Finnish (FIN) AF: 0.974 AC: 10351 AN: 10624

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 0.996 AC: 67756 AN: 68048

Other (OTH) AF: 0.997 AC: 2108 AN: 2114

Alfa AF: 0.996 Hom.: 8925

Bravo AF: 0.997

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.5
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs135559; hg19: chr22-46539706;