ENST00000782365.1:n.523A>T

Variant names:

• chr1-12165294-T-A
• rs652625
• ENST00000782365.1:n.523A>T

Variant summary

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

The ENST00000782365.1(ENSG00000301863):​n.523A>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 0.131 in 152,110 control chromosomes in the GnomAD database, including 2,345 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 0.13 (2345 hom., cov: 32)
• Consequence: ENSG00000301863 ENST00000782365.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478
• Publications: 24 publications found

Genes affected

ENSG00000301863 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301863	ENST00000782365.1	n.523A>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19827 AN: 151992 Hom.: 2329 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0614

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.0139

Gnomad SAS AF: 0.0332

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0648

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.131 AC: 19902 AN: 152110 Hom.: 2345 Cov.: 32 AF XY: 0.125 AC XY: 9293 AN XY: 74358

African (AFR) AF: 0.320 AC: 13246 AN: 41434

American (AMR) AF: 0.0612 AC: 937 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0444 AC: 154 AN: 3468

East Asian (EAS) AF: 0.0139 AC: 72 AN: 5174

South Asian (SAS) AF: 0.0324 AC: 156 AN: 4820

European-Finnish (FIN) AF: 0.0532 AC: 564 AN: 10610

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0648 AC: 4403 AN: 67988

Other (OTH) AF: 0.120 AC: 254 AN: 2112

Alfa AF: 0.0956 Hom.: 160

Bravo AF: 0.139

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.48
DANN	Benign	0.77
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs652625; hg19: chr1-12225351; COSMIC: COSV66163762;