chr13-106191260-A-G

Variant names:

• chr13-106191260-A-G
• rs2165723
• ENST00000754737.1:n.128+22541T>C

Variant summary

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

The ENST00000754737.1(ENSG00000287923):​n.128+22541T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 152,116 control chromosomes in the GnomAD database, including 27,691 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 0.57 (27691 hom., cov: 33)
• Consequence: ENSG00000287923 ENST00000754737.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 3 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.709 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	ENST00000754737.1	n.128+22541T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87019 AN: 151998 Hom.: 27690 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.572 AC: 87036 AN: 152116 Hom.: 27691 Cov.: 33 AF XY: 0.574 AC XY: 42673 AN XY: 74358

African (AFR) AF: 0.272 AC: 11299 AN: 41528

American (AMR) AF: 0.627 AC: 9565 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2672 AN: 3470

East Asian (EAS) AF: 0.448 AC: 2310 AN: 5158

South Asian (SAS) AF: 0.702 AC: 3386 AN: 4824

European-Finnish (FIN) AF: 0.667 AC: 7063 AN: 10586

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48554 AN: 67976

Other (OTH) AF: 0.606 AC: 1282 AN: 2116

Alfa AF: 0.518 Hom.: 1881

Bravo AF: 0.551

Asia WGS AF: 0.557 AC: 1937 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.48
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs2165723; hg19: chr13-106843609;