ENST00000676649.1:n.447-18054T>C

Variant names:

• chr4-62202277-T-C
• rs1563796
• ENST00000676649.1:n.447-18054T>C

Variant summary

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

The ENST00000676649.1(ENSG00000288659):​n.447-18054T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,930 control chromosomes in the GnomAD database, including 29,571 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 (29571 hom., cov: 31)
• Consequence: ENSG00000288659 ENST00000676649.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593
• Publications: 2 publications found

Genes affected

ENSG00000288659 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927145	XR_938809.3	n.372-18054T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288659	ENST00000676649.1	n.447-18054T>C		intron_variant	Intron 3 of 3
ENSG00000288659	ENST00000687436.3	n.416-18054T>C		intron_variant	Intron 2 of 2
ENSG00000288659	ENST00000702460.2	n.287-12372T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93055 AN: 151812 Hom.: 29560 Cov.: 31

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.613 AC: 93094 AN: 151930 Hom.: 29571 Cov.: 31 AF XY: 0.613 AC XY: 45530 AN XY: 74280

African (AFR) AF: 0.454 AC: 18809 AN: 41426

American (AMR) AF: 0.633 AC: 9668 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2554 AN: 3468

East Asian (EAS) AF: 0.395 AC: 2032 AN: 5148

South Asian (SAS) AF: 0.680 AC: 3277 AN: 4816

European-Finnish (FIN) AF: 0.671 AC: 7070 AN: 10542

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47586 AN: 67946

Other (OTH) AF: 0.600 AC: 1265 AN: 2108

Alfa AF: 0.671 Hom.: 127476

Bravo AF: 0.600

Asia WGS AF: 0.508 AC: 1767 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.46
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs1563796; hg19: chr4-63067995;