rs10824896

Positions:

• chr10-50033327-C-G

Variant summary

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

The NR_038275.2(FAM21EP):​n.1892-11860G>C 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 0.131 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 NR_038275.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM21EP	NR_038275.2	n.1892-11860G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM21EP	ENST00000456967.5	n.1892-11860G>C		intron_variant, non_coding_transcript_variant		2
FAM21EP	ENST00000649244.1	n.843-11860G>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0743

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.0796

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.148

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10824896; hg19: chr10-51793087;