rs10507529

Positions:

• chr13-44315927-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_001749973.2(LOC107984552):​n.851-721A>G variant causes a intron, non coding transcript 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: LOC107984552 XR_001749973.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

Genes affected

LOC107984552 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 52 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984552	XR_001749973.2	n.851-721A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0402

Gnomad4 AMR AF: 0.0322

Gnomad4 ASJ AF: 0.0303

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0213

Gnomad4 FIN AF: 0.0128

Gnomad4 NFE AF: 0.0102

Gnomad4 OTH AF: 0.0170

Alfa AF: 0.0146 Hom.: 27

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507529; hg19: chr13-44890063;