22-50538325-T-C

Variant names:

• chr22-50538325-T-C
• rs131788
• ENST00000739822.1:n.241A>G

Variant summary

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

The ENST00000739822.1(ENSG00000296469):​n.241A>G 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 0.775 in 152,056 control chromosomes in the GnomAD database, including 46,072 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 0.78 (46072 hom., cov: 31)
• Consequence: ENSG00000296469 ENST00000739822.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 11 publications found

Genes affected

ENSG00000296469 (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 (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000739822.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296469	ENST00000739822.1		n.241A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000296469	ENST00000739823.1		n.163A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000296451	ENST00000739695.1		n.187-201T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117767 AN: 151938 Hom.: 46036 Cov.: 31

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.775 AC: 117861 AN: 152056 Hom.: 46072 Cov.: 31 AF XY: 0.782 AC XY: 58101 AN XY: 74330

African (AFR) AF: 0.816 AC: 33871 AN: 41494

American (AMR) AF: 0.773 AC: 11797 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2233 AN: 3462

East Asian (EAS) AF: 0.982 AC: 5077 AN: 5170

South Asian (SAS) AF: 0.864 AC: 4170 AN: 4824

European-Finnish (FIN) AF: 0.809 AC: 8548 AN: 10570

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.730 AC: 49589 AN: 67956

Other (OTH) AF: 0.746 AC: 1574 AN: 2110

Alfa AF: 0.750 Hom.: 63258

Bravo AF: 0.775

Asia WGS AF: 0.918 AC: 3193 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	0.83
DANN	Benign	0.36
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs131788; hg19: chr22-50976754;