chr13-106033224-A-G

Variant names:

• chr13-106033224-A-G
• rs9301099
• ENST00000657278.1:n.1795+29051T>C

Variant summary

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

The ENST00000657278.1(ENSG00000287923):​n.1795+29051T>C variant causes a intron change. The variant allele was found at a frequency of 0.194 in 152,102 control chromosomes in the GnomAD database, including 2,949 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 0.19 (2949 hom., cov: 32)
• Consequence: ENSG00000287923 ENST00000657278.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.00
• Publications: 3 publications found

Genes affected

ENSG00000287923 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 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.1795+29051T>C		intron_variant	Intron 1 of 2
ENSG00000287923	ENST00000670458.1	n.1562+29051T>C		intron_variant	Intron 1 of 2
ENSG00000287923	ENST00000754737.1	n.415+57284T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29461 AN: 151984 Hom.: 2938 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0357

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.194 AC: 29489 AN: 152102 Hom.: 2949 Cov.: 32 AF XY: 0.192 AC XY: 14264 AN XY: 74356

African (AFR) AF: 0.235 AC: 9765 AN: 41474

American (AMR) AF: 0.147 AC: 2253 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 673 AN: 3468

East Asian (EAS) AF: 0.0358 AC: 185 AN: 5172

South Asian (SAS) AF: 0.188 AC: 907 AN: 4822

European-Finnish (FIN) AF: 0.222 AC: 2352 AN: 10586

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12749 AN: 67986

Other (OTH) AF: 0.179 AC: 377 AN: 2110

Alfa AF: 0.184 Hom.: 11293

Bravo AF: 0.187

Asia WGS AF: 0.123 AC: 433 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	16
DANN	Benign	0.80
PhyloP100		4.0

Splicing

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

Other links and lift over

dbSNP: rs9301099; hg19: chr13-106685573;