13-20364901-C-T

Variant names:

• chr13-20364901-C-T
• rs944014
• ENST00000737490.1:n.380-6415C>T

Variant summary

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

The ENST00000737490.1(ENSG00000296234):​n.380-6415C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.879 in 152,210 control chromosomes in the GnomAD database, including 59,337 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 0.88 (59337 hom., cov: 33)
• Consequence: ENSG00000296234 ENST00000737490.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 2 publications found

Genes affected

ENSG00000296234 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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
ENSG00000296234	ENST00000737490.1	n.380-6415C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133626 AN: 152092 Hom.: 59298 Cov.: 33

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.984

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.879 AC: 133720 AN: 152210 Hom.: 59337 Cov.: 33 AF XY: 0.881 AC XY: 65524 AN XY: 74414

African (AFR) AF: 0.748 AC: 31016 AN: 41484

American (AMR) AF: 0.920 AC: 14076 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 3126 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5175 AN: 5180

South Asian (SAS) AF: 0.983 AC: 4746 AN: 4828

European-Finnish (FIN) AF: 0.898 AC: 9519 AN: 10600

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.927 AC: 63085 AN: 68030

Other (OTH) AF: 0.877 AC: 1853 AN: 2114

Alfa AF: 0.894 Hom.: 10652

Bravo AF: 0.872

Asia WGS AF: 0.975 AC: 3391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.17
DANN	Benign	0.34
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs944014; hg19: chr13-20939040;