4-14442514-C-T

Variant names:

• chr4-14442514-C-T
• rs218783
• ENST00000654462.1:n.425-8351C>T

Variant summary

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

The ENST00000654462.1(ENSG00000287360):​n.425-8351C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 148,980 control chromosomes in the GnomAD database, including 15,214 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 0.45 (15214 hom., cov: 27)
• Consequence: ENSG00000287360 ENST00000654462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• Publications: 3 publications found

Genes affected

ENSG00000287360 (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 (NFE) allele frequency at 95% confidence interval = 0.493 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
ENSG00000287360	ENST00000654462.1	n.425-8351C>T		intron_variant	Intron 1 of 2
ENSG00000287360	ENST00000723358.1	n.418-71093C>T		intron_variant	Intron 1 of 4
ENSG00000287360	ENST00000723359.1	n.452-4611C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.448 AC: 66672 AN: 148886 Hom.: 15211 Cov.: 27

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.470

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.448 AC: 66694 AN: 148980 Hom.: 15214 Cov.: 27 AF XY: 0.450 AC XY: 32595 AN XY: 72490

African (AFR) AF: 0.359 AC: 14400 AN: 40096

American (AMR) AF: 0.454 AC: 6782 AN: 14924

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1642 AN: 3468

East Asian (EAS) AF: 0.411 AC: 2079 AN: 5054

South Asian (SAS) AF: 0.351 AC: 1656 AN: 4722

European-Finnish (FIN) AF: 0.503 AC: 4954 AN: 9852

Middle Eastern (MID) AF: 0.475 AC: 133 AN: 280

European-Non Finnish (NFE) AF: 0.498 AC: 33648 AN: 67622

Other (OTH) AF: 0.468 AC: 962 AN: 2056

Alfa AF: 0.473 Hom.: 9040

Bravo AF: 0.436

Asia WGS AF: 0.351 AC: 1222 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	3.3
DANN	Benign	0.55
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs218783; hg19: chr4-14444138;