chr21-44712970-G-T

Variant names:

• chr21-44712970-G-T
• rs932281

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 0.268 in 151,662 control chromosomes in the GnomAD database, including 5,761 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 0.27 (5761 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 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: 0.268 AC: 40578 AN: 151540 Hom.: 5760 Cov.: 31

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.0253

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.268 AC: 40577 AN: 151662 Hom.: 5761 Cov.: 31 AF XY: 0.264 AC XY: 19600 AN XY: 74124

African (AFR) AF: 0.264 AC: 10907 AN: 41304

American (AMR) AF: 0.235 AC: 3591 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1026 AN: 3468

East Asian (EAS) AF: 0.0253 AC: 130 AN: 5132

South Asian (SAS) AF: 0.176 AC: 844 AN: 4796

European-Finnish (FIN) AF: 0.263 AC: 2776 AN: 10552

Middle Eastern (MID) AF: 0.245 AC: 71 AN: 290

European-Non Finnish (NFE) AF: 0.301 AC: 20407 AN: 67850

Other (OTH) AF: 0.290 AC: 609 AN: 2100

Alfa AF: 0.284 Hom.: 9998

Bravo AF: 0.268

Asia WGS AF: 0.145 AC: 507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.38
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs932281; hg19: chr21-46132885;