rs463055

chr21-26244283-C-T

Variant summary

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

The ENST00000701473.1(ENSG00000289899):n.98-19336G>A 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 0.362 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: ENST00000701473.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379

Genes affected

(HGNC:):

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 = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701473.1	n.98-19336G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.371

Alfa AF: 0.321 Hom.: 3732

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs463055; hg19: chr21-27616602;