rs2801272

Variant names:

• chr21-13289671-T-C
• rs2801272

Variant summary

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

The variant allele was found at a frequency of 0.58 in 151,744 control chromosomes in the GnomAD database, including 26,106 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 0.58 (26106 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 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

Frequencies

GnomAD3 genomes AF: 0.580 AC: 87894 AN: 151626 Hom.: 26064 Cov.: 31

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.580 AC: 87997 AN: 151744 Hom.: 26106 Cov.: 31 AF XY: 0.579 AC XY: 42969 AN XY: 74166

African (AFR) AF: 0.639 AC: 26428 AN: 41330

American (AMR) AF: 0.633 AC: 9640 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2225 AN: 3466

East Asian (EAS) AF: 0.773 AC: 3995 AN: 5166

South Asian (SAS) AF: 0.561 AC: 2704 AN: 4820

European-Finnish (FIN) AF: 0.506 AC: 5325 AN: 10526

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35811 AN: 67906

Other (OTH) AF: 0.602 AC: 1267 AN: 2106

Alfa AF: 0.544 Hom.: 2857

Bravo AF: 0.596

Asia WGS AF: 0.657 AC: 2287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.5
DANN	Benign	0.30
PhyloP100		-0.073

Splicing

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

Other links and lift over

dbSNP: rs2801272; hg19: chr21-14661992;