rs1924397

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr13-105960117-C-A
• chr13-105960117-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000287923 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.921

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.908

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.881

Gnomad4 OTH AF: 0.850

Alfa AF: 0.854 Hom.: 21662

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1924397; hg19: chr13-106612466;