rs1072869

Variant names:

• chr21-41285621-A-C
• rs1072869
• ENST00000754075.1:n.446-3005T>G

Variant summary

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

The ENST00000754075.1(ENSG00000298244):​n.446-3005T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,976 control chromosomes in the GnomAD database, including 10,880 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 0.37 (10880 hom., cov: 31)
• Consequence: ENSG00000298244 ENST00000754075.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822
• Publications: 7 publications found

Genes affected

ENSG00000298244 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.652 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
ENSG00000298244	ENST00000754075.1	n.446-3005T>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56540 AN: 151858 Hom.: 10866 Cov.: 31

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.372 AC: 56581 AN: 151976 Hom.: 10880 Cov.: 31 AF XY: 0.381 AC XY: 28273 AN XY: 74246

African (AFR) AF: 0.357 AC: 14786 AN: 41448

American (AMR) AF: 0.355 AC: 5424 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1101 AN: 3466

East Asian (EAS) AF: 0.671 AC: 3456 AN: 5154

South Asian (SAS) AF: 0.515 AC: 2480 AN: 4820

European-Finnish (FIN) AF: 0.413 AC: 4351 AN: 10544

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23861 AN: 67950

Other (OTH) AF: 0.372 AC: 786 AN: 2112

Alfa AF: 0.361 Hom.: 12718

Bravo AF: 0.371

Asia WGS AF: 0.546 AC: 1900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.68
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs1072869; hg19: chr21-42657548;