ENST00000745365.1:n.539+2296G>A

Variant names:

• chr8-131041906-G-A
• rs3829210
• ENST00000745365.1:n.539+2296G>A

Variant summary

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

The ENST00000745365.1(ENSG00000297096):​n.539+2296G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 152,178 control chromosomes in the GnomAD database, including 15,737 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 (15732 hom., cov: 34)
  • Exomes 𝑓: 0.47 (5 hom.)
• Consequence: ENSG00000297096 ENST00000745365.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• 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=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000745365.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297096	ENST00000745365.1		n.539+2296G>A		intron	N/A
	ENSG00000297096	ENST00000745366.1		n.98+2296G>A		intron	N/A
	ENSG00000297096	ENST00000745367.1		n.99+1491G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67651 AN: 152024 Hom.: 15733 Cov.: 34

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.448

GnomAD4 exome AF: 0.472 AC: 17 AN: 36 Hom.: 5 Cov.: 0 AF XY: 0.500 AC XY: 14 AN XY: 28

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.467 AC: 14 AN: 30

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.445 AC: 67671 AN: 152142 Hom.: 15732 Cov.: 34 AF XY: 0.452 AC XY: 33635 AN XY: 74360

African (AFR) AF: 0.307 AC: 12761 AN: 41524

American (AMR) AF: 0.479 AC: 7323 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1490 AN: 3470

East Asian (EAS) AF: 0.632 AC: 3248 AN: 5136

South Asian (SAS) AF: 0.547 AC: 2641 AN: 4824

European-Finnish (FIN) AF: 0.527 AC: 5592 AN: 10608

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33222 AN: 67970

Other (OTH) AF: 0.450 AC: 951 AN: 2114

Alfa AF: 0.480 Hom.: 35690

Bravo AF: 0.432

Asia WGS AF: 0.570 AC: 1982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	3.8
DANN	Benign	0.93
PhyloP100		-0.23
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3829210; hg19: chr8-132054152;