ENST00000758786.1:n.253+3696A>G

Variant names:

• chr7-152638744-A-G
• rs718282
• ENST00000758786.1:n.253+3696A>G

Variant summary

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

The ENST00000758786.1(ENSG00000298894):​n.253+3696A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.938 in 151,376 control chromosomes in the GnomAD database, including 66,691 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 0.94 (66691 hom., cov: 26)
• Consequence: ENSG00000298894 ENST00000758786.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 17 publications found

Genes affected

ENSG00000298894 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.939 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
ENSG00000298894	ENST00000758786.1	n.253+3696A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.938 AC: 141937 AN: 151258 Hom.: 66636 Cov.: 26

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.946

Gnomad ASJ AF: 0.928

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.929

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

GnomAD4 genome AF: 0.938 AC: 142048 AN: 151376 Hom.: 66691 Cov.: 26 AF XY: 0.940 AC XY: 69430 AN XY: 73892

African (AFR) AF: 0.923 AC: 38082 AN: 41266

American (AMR) AF: 0.946 AC: 14371 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.928 AC: 3219 AN: 3470

East Asian (EAS) AF: 0.874 AC: 4405 AN: 5040

South Asian (SAS) AF: 0.944 AC: 4505 AN: 4772

European-Finnish (FIN) AF: 0.983 AC: 10293 AN: 10468

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.945 AC: 64144 AN: 67868

Other (OTH) AF: 0.927 AC: 1947 AN: 2100

Alfa AF: 0.939 Hom.: 8678

Bravo AF: 0.933

Asia WGS AF: 0.908 AC: 3159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.7
DANN	Benign	0.38
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs718282; hg19: chr7-152335829;