13-73398244-C-T

Variant names:

• chr13-73398244-C-T
• rs1411318
• ENST00000782633.1:n.293-786C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000782633.1(ENSG00000279754):​n.293-786C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.931 in 152,282 control chromosomes in the GnomAD database, including 66,207 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 0.93 (66207 hom., cov: 33)
• Consequence: ENSG00000279754 ENST00000782633.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 1 publications found

Genes affected

ENSG00000279754 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782633.1. 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
	ENSG00000279754	ENST00000782633.1		n.293-786C>T		intron	N/A
	ENSG00000279754	ENST00000782634.1		n.193-786C>T		intron	N/A
	ENSG00000279754	ENST00000782635.1		n.211-786C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.931 AC: 141645 AN: 152164 Hom.: 66156 Cov.: 33

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.953

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.964

Gnomad OTH AF: 0.937

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

GnomAD4 genome AF: 0.931 AC: 141753 AN: 152282 Hom.: 66207 Cov.: 33 AF XY: 0.929 AC XY: 69151 AN XY: 74458

African (AFR) AF: 0.885 AC: 36761 AN: 41550

American (AMR) AF: 0.961 AC: 14699 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.953 AC: 3306 AN: 3468

East Asian (EAS) AF: 0.706 AC: 3650 AN: 5170

South Asian (SAS) AF: 0.906 AC: 4376 AN: 4832

European-Finnish (FIN) AF: 0.967 AC: 10260 AN: 10606

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.964 AC: 65603 AN: 68034

Other (OTH) AF: 0.938 AC: 1984 AN: 2116

Alfa AF: 0.958 Hom.: 29771

Bravo AF: 0.927

Asia WGS AF: 0.829 AC: 2883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	4.6
DANN	Benign	0.92
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1411318; hg19: chr13-73972381;