ENST00000759543.1:n.435+2493C>T

Variant names:

• chr3-65162946-G-A
• rs10510933
• ENST00000759543.1:n.435+2493C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000759543.1(ENSG00000298971):​n.435+2493C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 151,948 control chromosomes in the GnomAD database, including 2,739 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 0.18 (2739 hom., cov: 32)
• Consequence: ENSG00000298971 ENST00000759543.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.485
• Publications: 3 publications found

Genes affected

ENSG00000298971 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000759543.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298971	ENST00000759543.1		n.435+2493C>T		intron	N/A
	ENSG00000298971	ENST00000759544.1		n.633+2493C>T		intron	N/A
	ENSG00000298971	ENST00000759545.1		n.441-1233C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27532 AN: 151830 Hom.: 2739 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.181 AC: 27537 AN: 151948 Hom.: 2739 Cov.: 32 AF XY: 0.188 AC XY: 13976 AN XY: 74272

African (AFR) AF: 0.118 AC: 4892 AN: 41482

American (AMR) AF: 0.154 AC: 2355 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 582 AN: 3472

East Asian (EAS) AF: 0.253 AC: 1300 AN: 5140

South Asian (SAS) AF: 0.205 AC: 989 AN: 4820

European-Finnish (FIN) AF: 0.335 AC: 3535 AN: 10540

Middle Eastern (MID) AF: 0.266 AC: 77 AN: 290

European-Non Finnish (NFE) AF: 0.195 AC: 13230 AN: 67922

Other (OTH) AF: 0.168 AC: 355 AN: 2110

Alfa AF: 0.183 Hom.: 5173

Bravo AF: 0.166

Asia WGS AF: 0.219 AC: 761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	11
DANN	Benign	0.55
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs10510933; hg19: chr3-65148621;