rs10507529

Variant names:

• chr13-44315927-A-G
• rs10507529
• ENST00000841879.1:n.188-721A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000841879.1(ENSG00000309535):​n.188-721A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0214 in 152,302 control chromosomes in the GnomAD database, including 52 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 0.021 (52 hom., cov: 33)
• Consequence: ENSG00000309535 ENST00000841879.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 1 publications found

Genes affected

ENSG00000309535 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0214 (3255/152302) while in subpopulation AFR AF = 0.0402 (1672/41546). AF 95% confidence interval is 0.0386. There are 52 homozygotes in GnomAd4. There are 1677 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 52 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984552	XR_001749973.2	n.851-721A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309535	ENST00000841879.1	n.188-721A>G		intron_variant	Intron 2 of 3
ENSG00000309535	ENST00000841880.1	n.395-721A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0213 AC: 3244 AN: 152184 Hom.: 52 Cov.: 33

Gnomad AFR AF: 0.0400

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0323

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0215

Gnomad FIN AF: 0.0128

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0103

Gnomad OTH AF: 0.0172

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

GnomAD4 genome AF: 0.0214 AC: 3255 AN: 152302 Hom.: 52 Cov.: 33 AF XY: 0.0225 AC XY: 1677 AN XY: 74484

African (AFR) AF: 0.0402 AC: 1672 AN: 41546

American (AMR) AF: 0.0322 AC: 492 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0303 AC: 105 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5178

South Asian (SAS) AF: 0.0213 AC: 103 AN: 4828

European-Finnish (FIN) AF: 0.0128 AC: 136 AN: 10622

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0102 AC: 697 AN: 68038

Other (OTH) AF: 0.0170 AC: 36 AN: 2114

Alfa AF: 0.0159 Hom.: 47

Bravo AF: 0.0236

Asia WGS AF: 0.0200 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	13
DANN	Benign	0.73
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs10507529; hg19: chr13-44890063;