21-30714005-G-T

Variant names:

• chr21-30714005-G-T
• rs2833017
• ENST00000731715.1:n.138-3300C>A

Variant summary

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

The ENST00000731715.1(ENSG00000295670):​n.138-3300C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 152,014 control chromosomes in the GnomAD database, including 24,850 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 0.57 (24850 hom., cov: 32)
• Consequence: ENSG00000295670 ENST00000731715.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.476
• Publications: 4 publications found

Genes affected

ENSG00000295670 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372773	XR_937655.3	n.408-6696C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295670	ENST00000731715.1	n.138-3300C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86316 AN: 151896 Hom.: 24814 Cov.: 32

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.568 AC: 86403 AN: 152014 Hom.: 24850 Cov.: 32 AF XY: 0.564 AC XY: 41897 AN XY: 74286

African (AFR) AF: 0.569 AC: 23589 AN: 41460

American (AMR) AF: 0.636 AC: 9710 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2144 AN: 3472

East Asian (EAS) AF: 0.308 AC: 1593 AN: 5172

South Asian (SAS) AF: 0.619 AC: 2984 AN: 4820

European-Finnish (FIN) AF: 0.493 AC: 5200 AN: 10548

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39130 AN: 67948

Other (OTH) AF: 0.607 AC: 1284 AN: 2116

Alfa AF: 0.579 Hom.: 14321

Bravo AF: 0.578

Asia WGS AF: 0.520 AC: 1811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
DANN	Benign	0.55
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs2833017; hg19: chr21-32086323;