ENST00000810420.1:n.503T>C

Variant names:

• chr22-28846485-T-C
• rs5762852
• ENST00000810420.1:n.503T>C

Variant summary

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

The ENST00000810420.1(ENSG00000226471):​n.503T>C 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 0.139 in 152,126 control chromosomes in the GnomAD database, including 1,927 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 0.14 (1927 hom., cov: 32)
• Consequence: ENSG00000226471 ENST00000810420.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.630
• Publications: 5 publications found

Genes affected

ENSG00000226471 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810420.1. 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
	ENSG00000226471	ENST00000810420.1		n.503T>C		non_coding_transcript_exon	Exon 4 of 6
	ENSG00000226471	ENST00000810422.1		n.426T>C		non_coding_transcript_exon	Exon 3 of 5
	ENSG00000226471	ENST00000810424.1		n.431T>C		non_coding_transcript_exon	Exon 3 of 4

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21150 AN: 152008 Hom.: 1927 Cov.: 32

Gnomad AFR AF: 0.0437

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.139 AC: 21156 AN: 152126 Hom.: 1927 Cov.: 32 AF XY: 0.145 AC XY: 10757 AN XY: 74374

African (AFR) AF: 0.0436 AC: 1809 AN: 41518

American (AMR) AF: 0.130 AC: 1982 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3472

East Asian (EAS) AF: 0.307 AC: 1589 AN: 5170

South Asian (SAS) AF: 0.385 AC: 1856 AN: 4818

European-Finnish (FIN) AF: 0.187 AC: 1976 AN: 10578

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10910 AN: 67992

Other (OTH) AF: 0.172 AC: 362 AN: 2108

Alfa AF: 0.0669 Hom.: 116

Bravo AF: 0.126

Asia WGS AF: 0.339 AC: 1180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	8.3
DANN	Benign	0.90
PhyloP100		0.63

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5762852;

hg19: chr22-29242473;