13-105960117-C-A

Variant names:

• chr13-105960117-C-A
• rs1924397
• ENST00000657278.1:n.1796-7122G>T

Variant summary

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

The ENST00000657278.1(ENSG00000287923):​n.1796-7122G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.803 in 152,004 control chromosomes in the GnomAD database, including 50,107 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 (50107 hom., cov: 31)
• Consequence: ENSG00000287923 ENST00000657278.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 2 publications found

Genes affected

ENSG00000287923 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.886 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
ENSG00000287923	ENST00000657278.1	n.1796-7122G>T		intron_variant	Intron 1 of 2
ENSG00000287923	ENST00000670458.1	n.1563-7122G>T		intron_variant	Intron 1 of 2
ENSG00000287923	ENST00000754737.1	n.416-7122G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.803 AC: 121984 AN: 151886 Hom.: 50101 Cov.: 31

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.803 AC: 122023 AN: 152004 Hom.: 50107 Cov.: 31 AF XY: 0.804 AC XY: 59699 AN XY: 74294

African (AFR) AF: 0.607 AC: 25160 AN: 41426

American (AMR) AF: 0.889 AC: 13576 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3197 AN: 3472

East Asian (EAS) AF: 0.863 AC: 4432 AN: 5134

South Asian (SAS) AF: 0.908 AC: 4377 AN: 4820

European-Finnish (FIN) AF: 0.803 AC: 8477 AN: 10562

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.881 AC: 59928 AN: 67994

Other (OTH) AF: 0.850 AC: 1795 AN: 2112

Alfa AF: 0.852 Hom.: 33482

Bravo AF: 0.802

Asia WGS AF: 0.833 AC: 2896 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.054
DANN	Benign	0.48
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1924397; hg19: chr13-106612466;