ENST00000728754.1:n.285+23848C>A

Variant names:

• chr3-162160925-C-A
• rs2089739
• ENST00000728754.1:n.285+23848C>A

Variant summary

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

The ENST00000728754.1(ENSG00000295235):​n.285+23848C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 152,064 control chromosomes in the GnomAD database, including 35,667 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 0.66 (35667 hom., cov: 32)
• Consequence: ENSG00000295235 ENST00000728754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787
• Publications: 2 publications found

Genes affected

ENSG00000295235 (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 (NFE) allele frequency at 95% confidence interval = 0.804 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
ENSG00000295235	ENST00000728754.1	n.285+23848C>A		intron_variant	Intron 3 of 7
ENSG00000295235	ENST00000728755.1	n.92+26060C>A		intron_variant	Intron 1 of 2
ENSG00000295235	ENST00000728756.1	n.64+23848C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99936 AN: 151946 Hom.: 35653 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.657 AC: 99978 AN: 152064 Hom.: 35667 Cov.: 32 AF XY: 0.654 AC XY: 48649 AN XY: 74330

African (AFR) AF: 0.366 AC: 15187 AN: 41440

American (AMR) AF: 0.655 AC: 9998 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2936 AN: 3470

East Asian (EAS) AF: 0.559 AC: 2885 AN: 5164

South Asian (SAS) AF: 0.777 AC: 3743 AN: 4820

European-Finnish (FIN) AF: 0.728 AC: 7704 AN: 10584

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55042 AN: 67994

Other (OTH) AF: 0.685 AC: 1447 AN: 2112

Alfa AF: 0.761 Hom.: 24647

Bravo AF: 0.634

Asia WGS AF: 0.638 AC: 2218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	0.81
DANN	Benign	0.77
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs2089739; hg19: chr3-161878713;