rs10507928

Variant names:

• chr13-82863073-T-G
• rs10507928
• ENST00000663739.1:n.299-84469A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663739.1(ENSG00000286385):​n.299-84469A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,192 control chromosomes in the GnomAD database, including 1,008 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 0.11 (1008 hom., cov: 32)
• Consequence: ENSG00000286385 ENST00000663739.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

Genes affected

ENSG00000286385 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.252 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
ENSG00000286385	ENST00000663739.1	n.299-84469A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16534 AN: 152072 Hom.: 1007 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.0865

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.0635

Gnomad FIN AF: 0.0754

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0987

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.109 AC: 16543 AN: 152192 Hom.: 1008 Cov.: 32 AF XY: 0.107 AC XY: 7983 AN XY: 74424

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0864

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.0630

Gnomad4 FIN AF: 0.0754

Gnomad4 NFE AF: 0.0987

Gnomad4 OTH AF: 0.124

Alfa AF: 0.103 Hom.: 783

Bravo AF: 0.111

Asia WGS AF: 0.161 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507928; hg19: chr13-83437208;