chr21-27765141-T-C

Variant names:

• chr21-27765141-T-C
• rs2831154

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 0.713 in 152,072 control chromosomes in the GnomAD database, including 40,902 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 0.71 (40902 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.943
• 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 (NFE) allele frequency at 95% confidence interval = 0.826 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: 0.713 AC: 108374 AN: 151952 Hom.: 40884 Cov.: 33

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.713 AC: 108419 AN: 152072 Hom.: 40902 Cov.: 33 AF XY: 0.717 AC XY: 53307 AN XY: 74324

African (AFR) AF: 0.444 AC: 18399 AN: 41462

American (AMR) AF: 0.759 AC: 11577 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2954 AN: 3472

East Asian (EAS) AF: 0.685 AC: 3534 AN: 5158

South Asian (SAS) AF: 0.831 AC: 4008 AN: 4822

European-Finnish (FIN) AF: 0.848 AC: 8974 AN: 10588

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.832 AC: 56570 AN: 68006

Other (OTH) AF: 0.732 AC: 1545 AN: 2112

Alfa AF: 0.755 Hom.: 5869

Bravo AF: 0.689

Asia WGS AF: 0.762 AC: 2651 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	0.68
DANN	Benign	0.45
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs2831154; hg19: chr21-29137460;