ENST00000757762.1:n.318-737C>A

Variant names:

• chr22-19733950-C-A
• rs5748411
• ENST00000757762.1:n.318-737C>A

Variant summary

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

The ENST00000757762.1(ENSG00000298759):​n.318-737C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,066 control chromosomes in the GnomAD database, including 16,838 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 0.44 (16838 hom., cov: 34)
• Consequence: ENSG00000298759 ENST00000757762.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.743
• Publications: 2 publications found

Genes affected

ENSG00000298759 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372861	XR_007068004.1	n.1780-737C>A		intron_variant	Intron 2 of 2
LOC105372861	XR_938005.3	n.1215-737C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298759	ENST00000757762.1	n.318-737C>A		intron_variant	Intron 2 of 2
ENSG00000298759	ENST00000757763.1	n.260-737C>A		intron_variant	Intron 2 of 2
ENSG00000298759	ENST00000757764.1	n.241-737C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66092 AN: 151948 Hom.: 16809 Cov.: 34

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.435 AC: 66165 AN: 152066 Hom.: 16838 Cov.: 34 AF XY: 0.442 AC XY: 32852 AN XY: 74342

African (AFR) AF: 0.685 AC: 28396 AN: 41464

American (AMR) AF: 0.488 AC: 7453 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1049 AN: 3466

East Asian (EAS) AF: 0.650 AC: 3353 AN: 5162

South Asian (SAS) AF: 0.392 AC: 1893 AN: 4830

European-Finnish (FIN) AF: 0.386 AC: 4084 AN: 10584

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18690 AN: 67964

Other (OTH) AF: 0.398 AC: 839 AN: 2110

Alfa AF: 0.350 Hom.: 3525

Bravo AF: 0.456

Asia WGS AF: 0.517 AC: 1795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.73
DANN	Benign	0.68
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs5748411; hg19: chr22-19721473; COSMIC: COSV68315055;