rs7319068

Variant names:

• chr13-23107522-G-T
• rs7319068
• ENST00000743290.1:n.228+567C>A

Variant summary

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

The ENST00000743290.1(ENSG00000296879):​n.228+567C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 152,160 control chromosomes in the GnomAD database, including 42,889 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 0.75 (42889 hom., cov: 32)
• Consequence: ENSG00000296879 ENST00000743290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631
• Publications: 3 publications found

Genes affected

ENSG00000296879 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 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
ENSG00000296879	ENST00000743290.1	n.228+567C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113479 AN: 152042 Hom.: 42847 Cov.: 32

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.746 AC: 113570 AN: 152160 Hom.: 42889 Cov.: 32 AF XY: 0.740 AC XY: 55018 AN XY: 74378

African (AFR) AF: 0.854 AC: 35464 AN: 41534

American (AMR) AF: 0.591 AC: 9038 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2761 AN: 3472

East Asian (EAS) AF: 0.813 AC: 4206 AN: 5172

South Asian (SAS) AF: 0.751 AC: 3621 AN: 4820

European-Finnish (FIN) AF: 0.639 AC: 6750 AN: 10566

Middle Eastern (MID) AF: 0.695 AC: 203 AN: 292

European-Non Finnish (NFE) AF: 0.726 AC: 49333 AN: 67988

Other (OTH) AF: 0.728 AC: 1540 AN: 2114

Alfa AF: 0.729 Hom.: 52384

Bravo AF: 0.745

Asia WGS AF: 0.774 AC: 2691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.068
DANN	Benign	0.42
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs7319068; hg19: chr13-23681661;