ENST00000648025.2:n.245+559T>C

Variant names:

• chr6-3877710-T-C
• rs10447475
• ENST00000648025.2:n.245+559T>C

Variant summary

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

The ENST00000648025.2(ENSG00000233068):​n.245+559T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 150,584 control chromosomes in the GnomAD database, including 9,252 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 0.34 (9252 hom., cov: 26)
• Consequence: ENSG00000233068 ENST00000648025.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 2 publications found

Genes affected

ENSG00000233068 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648025.2. 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
	ENSG00000233068	ENST00000648025.2		n.245+559T>C		intron	N/A
	ENSG00000233068	ENST00000780356.1		n.205+559T>C		intron	N/A
	ENSG00000233068	ENST00000780357.1		n.119-15352T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.339 AC: 50961 AN: 150474 Hom.: 9257 Cov.: 26

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.339 AC: 50984 AN: 150584 Hom.: 9252 Cov.: 26 AF XY: 0.340 AC XY: 24987 AN XY: 73478

African (AFR) AF: 0.334 AC: 13711 AN: 41070

American (AMR) AF: 0.464 AC: 6995 AN: 15086

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1361 AN: 3462

East Asian (EAS) AF: 0.602 AC: 3055 AN: 5078

South Asian (SAS) AF: 0.410 AC: 1944 AN: 4740

European-Finnish (FIN) AF: 0.206 AC: 2136 AN: 10360

Middle Eastern (MID) AF: 0.379 AC: 110 AN: 290

European-Non Finnish (NFE) AF: 0.306 AC: 20660 AN: 67520

Other (OTH) AF: 0.374 AC: 774 AN: 2072

Alfa AF: 0.316 Hom.: 1097

Bravo AF: 0.359

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.44
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs10447475; hg19: chr6-3877944;