rs10519953

Variant names:

• chr5-127668997-G-A
• rs10519953
• ENST00000827053.1:n.195-5229C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-127668997-G-A
• chr5-127668997-G-C

Variant summary

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

The ENST00000827053.1(ENSG00000248799):​n.195-5229C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,928 control chromosomes in the GnomAD database, including 29,122 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 0.61 (29122 hom., cov: 31)
• Consequence: ENSG00000248799 ENST00000827053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946
• Publications: 1 publications found

Genes affected

ENSG00000248799 (HGNC:59127):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.652 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.195-5229C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93074 AN: 151810 Hom.: 29080 Cov.: 31

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.613 AC: 93158 AN: 151928 Hom.: 29122 Cov.: 31 AF XY: 0.607 AC XY: 45037 AN XY: 74242

African (AFR) AF: 0.622 AC: 25746 AN: 41420

American (AMR) AF: 0.489 AC: 7454 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2055 AN: 3472

East Asian (EAS) AF: 0.355 AC: 1836 AN: 5166

South Asian (SAS) AF: 0.485 AC: 2332 AN: 4804

European-Finnish (FIN) AF: 0.670 AC: 7068 AN: 10548

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.657 AC: 44626 AN: 67946

Other (OTH) AF: 0.590 AC: 1247 AN: 2112

Alfa AF: 0.615 Hom.: 5069

Bravo AF: 0.597

Asia WGS AF: 0.404 AC: 1409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.19
DANN	Benign	0.66
PhyloP100		-0.95

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10519953;

hg19: chr5-127004689;