rs463055

Variant names:

• chr21-26244283-C-T
• rs463055
• ENST00000701473.1:n.98-19336G>A

Variant summary

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

The ENST00000701473.1(ENSG00000289899):​n.98-19336G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,002 control chromosomes in the GnomAD database, including 10,342 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 0.36 (10342 hom., cov: 33)
• Consequence: ENSG00000289899 ENST00000701473.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379
• Publications: 1 publications found

Genes affected

ENSG00000289899 (HGNC:):

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 = 0.563 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
ENSG00000289899	ENST00000701473.1	n.98-19336G>A		intron_variant	Intron 1 of 1
ENSG00000289899	ENST00000747828.1	n.193-1664G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54957 AN: 151884 Hom.: 10325 Cov.: 33

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.362 AC: 55016 AN: 152002 Hom.: 10342 Cov.: 33 AF XY: 0.365 AC XY: 27117 AN XY: 74278

African (AFR) AF: 0.433 AC: 17933 AN: 41436

American (AMR) AF: 0.354 AC: 5401 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1083 AN: 3472

East Asian (EAS) AF: 0.580 AC: 3000 AN: 5168

South Asian (SAS) AF: 0.381 AC: 1833 AN: 4816

European-Finnish (FIN) AF: 0.356 AC: 3759 AN: 10546

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.308 AC: 20945 AN: 67970

Other (OTH) AF: 0.371 AC: 785 AN: 2116

Alfa AF: 0.322 Hom.: 4171

Bravo AF: 0.368

Asia WGS AF: 0.492 AC: 1713 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	5.3
DANN	Benign	0.51
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs463055; hg19: chr21-27616602;