ENST00000745365.1:n.755-63966A>G

Variant names:

• chr8-131225922-A-G
• rs4523235
• ENST00000745365.1:n.755-63966A>G

Variant summary

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

The ENST00000745365.1(ENSG00000297096):​n.755-63966A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,078 control chromosomes in the GnomAD database, including 6,124 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 0.28 (6124 hom., cov: 32)
• Consequence: ENSG00000297096 ENST00000745365.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 4 publications found

Genes affected

ENSG00000297096 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375760	XR_007061183.1	n.435-63966A>G		intron_variant	Intron 4 of 5
LOC105375760	XR_928653.3	n.297-63966A>G		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297096	ENST00000745365.1	n.755-63966A>G		intron_variant	Intron 3 of 3
ENSG00000297096	ENST00000745366.1	n.314-47330A>G		intron_variant	Intron 3 of 5
ENSG00000297096	ENST00000745367.1	n.315-63966A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42443 AN: 151960 Hom.: 6102 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.280 AC: 42517 AN: 152078 Hom.: 6124 Cov.: 32 AF XY: 0.273 AC XY: 20297 AN XY: 74344

African (AFR) AF: 0.314 AC: 13048 AN: 41494

American (AMR) AF: 0.224 AC: 3425 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3470

East Asian (EAS) AF: 0.170 AC: 878 AN: 5162

South Asian (SAS) AF: 0.254 AC: 1222 AN: 4818

European-Finnish (FIN) AF: 0.238 AC: 2513 AN: 10566

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.292 AC: 19871 AN: 67976

Other (OTH) AF: 0.255 AC: 538 AN: 2108

Alfa AF: 0.282 Hom.: 20027

Bravo AF: 0.278

Asia WGS AF: 0.209 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.1
DANN	Benign	0.41
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4523235; hg19: chr8-132238169;