13-39111430-C-T

Variant names:

• chr13-39111430-C-T
• rs1409440
• ENST00000614005.1:n.257+58102C>T

Variant summary

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

The ENST00000614005.1(ENSG00000273507):​n.257+58102C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 152,080 control chromosomes in the GnomAD database, including 52,526 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 0.82 (52526 hom., cov: 31)
• Consequence: ENSG00000273507 ENST00000614005.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367

Genes affected

ENSG00000273507 (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 (EAS) allele frequency at 95% confidence interval = 0.964 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
ENSG00000273507	ENST00000614005.1	n.257+58102C>T		intron_variant	Intron 1 of 2	3
ENSG00000273507	ENST00000655342.1	n.256+58102C>T		intron_variant	Intron 1 of 2
ENSG00000273507	ENST00000655935.1	n.286-7801C>T		intron_variant	Intron 1 of 1
ENSG00000273507	ENST00000668183.1	n.258-57961C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124212 AN: 151962 Hom.: 52511 Cov.: 31

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.817 AC: 124270 AN: 152080 Hom.: 52526 Cov.: 31 AF XY: 0.818 AC XY: 60822 AN XY: 74346

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.906

Gnomad4 ASJ AF: 0.902

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.911

Gnomad4 NFE AF: 0.907

Gnomad4 OTH AF: 0.860

Alfa AF: 0.898 Hom.: 114570

Bravo AF: 0.809

Asia WGS AF: 0.906 AC: 3151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1409440; hg19: chr13-39685567;