13-107047870-T-C

Variant names:

• chr13-107047870-T-C
• rs9558942
• ENST00000765296.1:n.85+11260A>G

Variant summary

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

The ENST00000765296.1(ENSG00000299637):​n.85+11260A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,124 control chromosomes in the GnomAD database, including 6,624 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 0.27 (6624 hom., cov: 33)
• Consequence: ENSG00000299637 ENST00000765296.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.645
• Publications: 7 publications found

Genes affected

ENSG00000299637 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 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
ENSG00000299637	ENST00000765296.1	n.85+11260A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40915 AN: 152006 Hom.: 6622 Cov.: 33

Gnomad AFR AF: 0.0997

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.269 AC: 40954 AN: 152124 Hom.: 6624 Cov.: 33 AF XY: 0.268 AC XY: 19914 AN XY: 74356

African (AFR) AF: 0.100 AC: 4160 AN: 41542

American (AMR) AF: 0.416 AC: 6353 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1318 AN: 3470

East Asian (EAS) AF: 0.492 AC: 2544 AN: 5168

South Asian (SAS) AF: 0.235 AC: 1132 AN: 4818

European-Finnish (FIN) AF: 0.199 AC: 2106 AN: 10588

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22196 AN: 67956

Other (OTH) AF: 0.342 AC: 722 AN: 2112

Alfa AF: 0.321 Hom.: 36585

Bravo AF: 0.284

Asia WGS AF: 0.332 AC: 1156 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.37
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs9558942; hg19: chr13-107700218;