ENST00000739695.1:n.186+1580T>C

Variant names:

• chr22-50532837-T-C
• rs140522
• ENST00000739695.1:n.186+1580T>C

Variant summary

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

The ENST00000739695.1(ENSG00000296451):​n.186+1580T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 151,906 control chromosomes in the GnomAD database, including 30,400 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 0.63 (30400 hom., cov: 32)
• Consequence: ENSG00000296451 ENST00000739695.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• Publications: 108 publications found

Genes affected

ENSG00000296451 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 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
ENSG00000296451	ENST00000739695.1	n.186+1580T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95059 AN: 151788 Hom.: 30408 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.626 AC: 95079 AN: 151906 Hom.: 30400 Cov.: 32 AF XY: 0.631 AC XY: 46847 AN XY: 74236

African (AFR) AF: 0.493 AC: 20397 AN: 41350

American (AMR) AF: 0.667 AC: 10184 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2390 AN: 3468

East Asian (EAS) AF: 0.707 AC: 3661 AN: 5178

South Asian (SAS) AF: 0.675 AC: 3251 AN: 4814

European-Finnish (FIN) AF: 0.706 AC: 7445 AN: 10538

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45537 AN: 67970

Other (OTH) AF: 0.622 AC: 1313 AN: 2112

Alfa AF: 0.656 Hom.: 135147

Bravo AF: 0.621

Asia WGS AF: 0.614 AC: 2136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.1
DANN	Benign	0.58
PhyloP100		-0.51
PromoterAI		0.0075	Neutral

Splicing

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

Other links and lift over

dbSNP: rs140522; hg19: chr22-50971266;