chr4-14442450-T-C

Variant names:

• chr4-14442450-T-C
• rs6840951
• ENST00000654462.1:n.425-8415T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654462.1(ENSG00000287360):​n.425-8415T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,732 control chromosomes in the GnomAD database, including 3,721 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 0.21 (3721 hom., cov: 31)
• Consequence: ENSG00000287360 ENST00000654462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.542

Genes affected

ENSG00000287360 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.312 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.425-8415T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31708 AN: 151616 Hom.: 3715 Cov.: 31

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.0889

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.209 AC: 31727 AN: 151732 Hom.: 3721 Cov.: 31 AF XY: 0.209 AC XY: 15473 AN XY: 74178

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.0889

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.174

Alfa AF: 0.184 Hom.: 644

Bravo AF: 0.216

Asia WGS AF: 0.242 AC: 841 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.3
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6840951; hg19: chr4-14444074;