ENST00000648455.1:n.353-12875T>A

Variant names:

• chr7-51651833-T-A
• rs6592945
• ENST00000648455.1:n.353-12875T>A

Variant summary

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

The ENST00000648455.1(ENSG00000285741):​n.353-12875T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 151,992 control chromosomes in the GnomAD database, including 28,570 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 0.61 (28570 hom., cov: 32)
• Consequence: ENSG00000285741 ENST00000648455.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100
• Publications: 3 publications found

Genes affected

ENSG00000285741 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 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
ENSG00000285741	ENST00000648455.1	n.353-12875T>A		intron_variant	Intron 2 of 6
ENSG00000285741	ENST00000769890.1	n.481-12875T>A		intron_variant	Intron 4 of 8
ENSG00000285741	ENST00000769891.1	n.470-12875T>A		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92284 AN: 151874 Hom.: 28535 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.608 AC: 92374 AN: 151992 Hom.: 28570 Cov.: 32 AF XY: 0.613 AC XY: 45518 AN XY: 74284

African (AFR) AF: 0.713 AC: 29519 AN: 41410

American (AMR) AF: 0.673 AC: 10286 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1921 AN: 3470

East Asian (EAS) AF: 0.633 AC: 3268 AN: 5166

South Asian (SAS) AF: 0.659 AC: 3179 AN: 4822

European-Finnish (FIN) AF: 0.554 AC: 5853 AN: 10556

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36421 AN: 67970

Other (OTH) AF: 0.628 AC: 1326 AN: 2110

Alfa AF: 0.570 Hom.: 3070

Bravo AF: 0.621

Asia WGS AF: 0.641 AC: 2227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.31
PhyloP100		-0.0010

Splicing

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

Other links and lift over

dbSNP: rs6592945; hg19: chr7-51719529;