rs10507580

chr13-53484981-A-G

Variant summary

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

The ENST00000657016.1(ENSG00000287722):n.629+180859A>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 0.0938 in 152,176 control chromosomes in the GnomAD database, including 960 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 0.094 (960 hom., cov: 32)
• Consequence: ENST00000657016.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000657016.1	n.629+180859A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0937 AC: 14245 AN: 152058 Hom.: 958 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0763

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.0644

Gnomad FIN AF: 0.0352

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0522

Gnomad OTH AF: 0.0794

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

GnomAD4 genome AF: 0.0938 AC: 14276 AN: 152176 Hom.: 960 Cov.: 32 AF XY: 0.0929 AC XY: 6913 AN XY: 74392

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.0764

Gnomad4 ASJ AF: 0.0516

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.0643

Gnomad4 FIN AF: 0.0352

Gnomad4 NFE AF: 0.0522

Gnomad4 OTH AF: 0.0781

Alfa AF: 0.0601 Hom.: 674

Bravo AF: 0.104

Asia WGS AF: 0.100 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.5
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507580; hg19: chr13-54059116;