chr13-39111430-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

ENSG00000273507 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000614005.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000273507	ENST00000614005.1	TSL:3	n.257+58102C>T		intron	N/A
	ENSG00000273507	ENST00000655342.1		n.256+58102C>T		intron	N/A
	ENSG00000273507	ENST00000655935.1		n.286-7801C>T		intron	N/A

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

African (AFR) AF: 0.574 AC: 23783 AN: 41446

American (AMR) AF: 0.906 AC: 13854 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.902 AC: 3132 AN: 3472

East Asian (EAS) AF: 0.986 AC: 5088 AN: 5158

South Asian (SAS) AF: 0.864 AC: 4157 AN: 4810

European-Finnish (FIN) AF: 0.911 AC: 9628 AN: 10574

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.907 AC: 61714 AN: 68008

Other (OTH) AF: 0.860 AC: 1817 AN: 2114

Alfa AF: 0.880 Hom.: 228059

Bravo AF: 0.809

Asia WGS AF: 0.906 AC: 3151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.90
PhyloP100		-0.37

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1409440;

hg19: chr13-39685567;