chr4-53799392-C-T

Variant names:

• chr4-53799392-C-T
• rs6851470
• ENST00000507166.5:c.1017+373427C>T

Variant summary

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

The ENST00000507166.5(ENSG00000282278):​c.1017+373427C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,074 control chromosomes in the GnomAD database, including 9,579 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 0.31 (9579 hom., cov: 33)
• Consequence: ENSG00000282278 ENST00000507166.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372

Genes affected

ENSG00000282278 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.582 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
ENSG00000282278	ENST00000507166.5	c.1017+373427C>T		intron_variant	Intron 12 of 23	2		ENSP00000423325.1

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46933 AN: 151956 Hom.: 9539 Cov.: 33

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.309 AC: 47025 AN: 152074 Hom.: 9579 Cov.: 33 AF XY: 0.300 AC XY: 22314 AN XY: 74346

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.281

Alfa AF: 0.242 Hom.: 2564

Bravo AF: 0.323

Asia WGS AF: 0.221 AC: 768 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	1.9
DANN	Benign	0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6851470; hg19: chr4-54665559;