4-159506641-C-T

Variant names:

• chr4-159506641-C-T
• rs1317266
• ENST00000818265.1:n.87-4270C>T

Variant summary

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

The ENST00000818265.1(ENSG00000306419):​n.87-4270C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 152,070 control chromosomes in the GnomAD database, including 48,445 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 0.80 (48445 hom., cov: 31)
• Consequence: ENSG00000306419 ENST00000818265.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 3 publications found

Genes affected

ENSG00000306419 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 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
ENSG00000306419	ENST00000818265.1	n.87-4270C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121189 AN: 151950 Hom.: 48408 Cov.: 31

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.777

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.798 AC: 121278 AN: 152070 Hom.: 48445 Cov.: 31 AF XY: 0.800 AC XY: 59439 AN XY: 74342

African (AFR) AF: 0.788 AC: 32690 AN: 41478

American (AMR) AF: 0.864 AC: 13212 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2851 AN: 3472

East Asian (EAS) AF: 0.867 AC: 4481 AN: 5168

South Asian (SAS) AF: 0.740 AC: 3571 AN: 4828

European-Finnish (FIN) AF: 0.794 AC: 8385 AN: 10564

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53364 AN: 67960

Other (OTH) AF: 0.788 AC: 1655 AN: 2100

Alfa AF: 0.783 Hom.: 23860

Bravo AF: 0.804

Asia WGS AF: 0.789 AC: 2745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.41
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs1317266; hg19: chr4-160427793;