ENST00000676649.1:n.447-25469T>C

Variant names:

• chr4-62194862-T-C
• rs4446347
• ENST00000676649.1:n.447-25469T>C

Variant summary

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

The ENST00000676649.1(ENSG00000288659):​n.447-25469T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 151,716 control chromosomes in the GnomAD database, including 28,201 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 (28201 hom., cov: 30)
• Consequence: ENSG00000288659 ENST00000676649.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927145	XR_938809.3	n.372-25469T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288659	ENST00000676649.1	n.447-25469T>C		intron_variant	Intron 3 of 3
ENSG00000288659	ENST00000687436.3	n.416-25469T>C		intron_variant	Intron 2 of 2
ENSG00000288659	ENST00000702460.2	n.287-19787T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91718 AN: 151596 Hom.: 28158 Cov.: 30

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.605 AC: 91821 AN: 151716 Hom.: 28201 Cov.: 30 AF XY: 0.603 AC XY: 44662 AN XY: 74126

African (AFR) AF: 0.697 AC: 28829 AN: 41374

American (AMR) AF: 0.620 AC: 9441 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2012 AN: 3472

East Asian (EAS) AF: 0.585 AC: 2986 AN: 5104

South Asian (SAS) AF: 0.485 AC: 2327 AN: 4798

European-Finnish (FIN) AF: 0.565 AC: 5937 AN: 10512

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.563 AC: 38269 AN: 67918

Other (OTH) AF: 0.619 AC: 1303 AN: 2106

Alfa AF: 0.581 Hom.: 32790

Bravo AF: 0.615

Asia WGS AF: 0.581 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.61
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs4446347; hg19: chr4-63060580;