ENST00000740104.1:n.237+1164C>G

Variant names:

• chr19-22352743-C-G
• rs8111537
• ENST00000740104.1:n.237+1164C>G

Variant summary

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

The ENST00000740104.1(ENSG00000296529):​n.237+1164C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 151,782 control chromosomes in the GnomAD database, including 24,090 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 0.56 (24090 hom., cov: 31)
• Consequence: ENSG00000296529 ENST00000740104.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.265
• Publications: 3 publications found

Genes affected

ENSG00000296529 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.732 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
ENSG00000296529	ENST00000740104.1	n.237+1164C>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85112 AN: 151664 Hom.: 24055 Cov.: 31

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.561 AC: 85204 AN: 151782 Hom.: 24090 Cov.: 31 AF XY: 0.568 AC XY: 42141 AN XY: 74150

African (AFR) AF: 0.556 AC: 23009 AN: 41364

American (AMR) AF: 0.571 AC: 8700 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2391 AN: 3472

East Asian (EAS) AF: 0.609 AC: 3130 AN: 5136

South Asian (SAS) AF: 0.752 AC: 3615 AN: 4806

European-Finnish (FIN) AF: 0.564 AC: 5928 AN: 10518

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.539 AC: 36591 AN: 67930

Other (OTH) AF: 0.587 AC: 1240 AN: 2112

Alfa AF: 0.404 Hom.: 1039

Bravo AF: 0.554

Asia WGS AF: 0.716 AC: 2490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.61
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs8111537; hg19: chr19-22535545;