rs10507580

Variant names:

• chr13-53484981-A-G
• rs10507580
• ENST00000657016.1:n.629+180859A>G

Variant summary

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

The ENST00000657016.1(ENSG00000287722):​n.629+180859A>G variant causes a intron 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: ENSG00000287722 ENST00000657016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• Publications: 3 publications found

Genes affected

ENSG00000287722 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287722	ENST00000657016.1	n.629+180859A>G		intron_variant	Intron 2 of 3
ENSG00000288768	ENST00000748644.1	n.714+14691A>G		intron_variant	Intron 5 of 6
ENSG00000288768	ENST00000748645.1	n.564+14691A>G		intron_variant	Intron 4 of 4

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

African (AFR) AF: 0.187 AC: 7752 AN: 41500

American (AMR) AF: 0.0764 AC: 1168 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3468

East Asian (EAS) AF: 0.138 AC: 712 AN: 5168

South Asian (SAS) AF: 0.0643 AC: 309 AN: 4806

European-Finnish (FIN) AF: 0.0352 AC: 374 AN: 10614

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0522 AC: 3549 AN: 68014

Other (OTH) AF: 0.0781 AC: 165 AN: 2112

Alfa AF: 0.0663 Hom.: 1912

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
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs10507580; hg19: chr13-54059116;