chr21-15444732-A-C

Variant names:

• chr21-15444732-A-C
• rs1297265
• ENST00000634644.1:n.952+22556T>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000634644.1(ENSG00000229425):​n.952+22556T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: ENSG00000229425 ENST00000634644.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524
• Publications: 41 publications found

Genes affected

ENSG00000229425 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927745	NR_188234.1	n.-76T>G		upstream_gene_variant
LOC101927745	NR_188235.1	n.-76T>G		upstream_gene_variant
LOC101927745	NR_188236.1	n.-76T>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229425	ENST00000634644.1	n.952+22556T>G		intron_variant	Intron 8 of 11	5
ENSG00000229425	ENST00000634708.1	n.423+33056T>G		intron_variant	Intron 3 of 9	5
ENSG00000229425	ENST00000654045.1	n.734-651T>G		intron_variant	Intron 5 of 9

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 42264

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	0.30
DANN	Benign	0.53
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs1297265; hg19: chr21-16817051;