rs10824896

Variant names:

• chr10-50033327-C-G
• rs10824896
• ENST00000456967.5:n.1892-11860G>C

Your query was ambiguous. Multiple possible variants found:

• chr10-50033327-C-G
• chr10-50033327-C-T

Variant summary

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

The ENST00000456967.5(FAM21EP):​n.1892-11860G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,256 control chromosomes in the GnomAD database, including 1,755 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 0.13 (1755 hom., cov: 33)
• Consequence: FAM21EP ENST00000456967.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 4 publications found

Genes affected

FAM21EP (HGNC:):

FAM21EP (HGNC:45010): (family with sequence similarity 21 member E, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456967.5. 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
	FAM21EP	NR_038275.2		n.1892-11860G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM21EP	ENST00000456967.5	TSL:2	n.1892-11860G>C		intron	N/A
	FAM21EP	ENST00000649244.2		n.1161-11860G>C		intron	N/A
	FAM21EP	ENST00000799271.1		n.876+14875G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19999 AN: 152138 Hom.: 1753 Cov.: 33

Gnomad AFR AF: 0.0744

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0796

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.131 AC: 20018 AN: 152256 Hom.: 1755 Cov.: 33 AF XY: 0.131 AC XY: 9764 AN XY: 74440

African (AFR) AF: 0.0743 AC: 3089 AN: 41562

American (AMR) AF: 0.259 AC: 3963 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 593 AN: 3466

East Asian (EAS) AF: 0.278 AC: 1433 AN: 5162

South Asian (SAS) AF: 0.168 AC: 812 AN: 4826

European-Finnish (FIN) AF: 0.0796 AC: 845 AN: 10612

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

European-Non Finnish (NFE) AF: 0.130 AC: 8868 AN: 68026

Other (OTH) AF: 0.148 AC: 313 AN: 2116

Alfa AF: 0.129 Hom.: 201

Bravo AF: 0.147

Asia WGS AF: 0.236 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.90
DANN	Benign	0.33
PhyloP100		0.20

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: rs10824896;

hg19: chr10-51793087;