rs9978551

Variant names:

• chr21-33018125-G-C
• rs9978551
• ENST00000454622.2:n.201+52779C>G

Variant summary

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

The ENST00000454622.2(ENSG00000227757):​n.201+52779C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0863 in 152,306 control chromosomes in the GnomAD database, including 662 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 0.086 (662 hom., cov: 33)
• Consequence: ENSG00000227757 ENST00000454622.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

ENSG00000227757 (HGNC:):

C21orf62-AS1 (HGNC:1290): (EPCIP antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.139 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
ENSG00000227757	ENST00000454622.2	n.201+52779C>G		intron_variant	Intron 1 of 1	2
C21orf62-AS1	ENST00000700822.1	n.487-1259G>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0862 AC: 13119 AN: 152188 Hom.: 660 Cov.: 33

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0804

Gnomad ASJ AF: 0.0447

Gnomad EAS AF: 0.0820

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0601

Gnomad OTH AF: 0.0826

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

GnomAD4 genome AF: 0.0863 AC: 13137 AN: 152306 Hom.: 662 Cov.: 33 AF XY: 0.0903 AC XY: 6727 AN XY: 74480

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.0807

Gnomad4 ASJ AF: 0.0447

Gnomad4 EAS AF: 0.0814

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.0601

Gnomad4 OTH AF: 0.0870

Alfa AF: 0.0802 Hom.: 79

Bravo AF: 0.0820

Asia WGS AF: 0.144 AC: 502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.30
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9978551; hg19: chr21-34390433;