rs10519957

Variant names:

• chr5-127697155-G-A
• rs10519957
• ENST00000827053.1:n.194+5572C>T

Variant summary

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

The ENST00000827053.1(ENSG00000248799):​n.194+5572C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0578 in 151,822 control chromosomes in the GnomAD database, including 571 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 0.058 (571 hom., cov: 32)
• Consequence: ENSG00000248799 ENST00000827053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• Publications: 1 publications found

Genes affected

ENSG00000248799 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827053.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248799	ENST00000827053.1		n.194+5572C>T		intron	N/A
	ENSG00000248799	ENST00000827054.1		n.198+12141C>T		intron	N/A
	ENSG00000248799	ENST00000827055.1		n.252+5572C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0577 AC: 8754 AN: 151704 Hom.: 570 Cov.: 32

Gnomad AFR AF: 0.0913

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0906

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.0817

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0106

Gnomad OTH AF: 0.0686

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

GnomAD4 genome AF: 0.0578 AC: 8768 AN: 151822 Hom.: 571 Cov.: 32 AF XY: 0.0608 AC XY: 4510 AN XY: 74194

African (AFR) AF: 0.0913 AC: 3779 AN: 41398

American (AMR) AF: 0.131 AC: 1987 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.0906 AC: 314 AN: 3464

East Asian (EAS) AF: 0.268 AC: 1379 AN: 5148

South Asian (SAS) AF: 0.0820 AC: 393 AN: 4794

European-Finnish (FIN) AF: 0.00104 AC: 11 AN: 10560

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0106 AC: 719 AN: 67926

Other (OTH) AF: 0.0717 AC: 151 AN: 2106

Alfa AF: 0.0356 Hom.: 37

Bravo AF: 0.0703

Asia WGS AF: 0.170 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.58
DANN	Benign	0.80
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs10519957; hg19: chr5-127032847;