21-34785401-C-T

Variant names:

• chr21-34785401-C-T
• rs2070370

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 0.373 in 151,948 control chromosomes in the GnomAD database, including 10,828 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 (10828 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.520
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.426 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: 0.373 AC: 56690 AN: 151830 Hom.: 10827 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.373 AC: 56708 AN: 151948 Hom.: 10828 Cov.: 32 AF XY: 0.376 AC XY: 27918 AN XY: 74236

African (AFR) AF: 0.287 AC: 11905 AN: 41434

American (AMR) AF: 0.383 AC: 5843 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1364 AN: 3472

East Asian (EAS) AF: 0.385 AC: 1984 AN: 5158

South Asian (SAS) AF: 0.441 AC: 2127 AN: 4818

European-Finnish (FIN) AF: 0.434 AC: 4572 AN: 10536

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27808 AN: 67942

Other (OTH) AF: 0.374 AC: 789 AN: 2108

Alfa AF: 0.401 Hom.: 53669

Bravo AF: 0.365

Asia WGS AF: 0.426 AC: 1478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.92
DANN	Benign	0.59
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs2070370; hg19: chr21-36157698;