rs7279521

Variant names:

• chr21-44985361-C-T
• rs7279521

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 0.216 in 152,160 control chromosomes in the GnomAD database, including 4,309 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 0.22 (4309 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.72
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 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: 0.216 AC: 32871 AN: 152042 Hom.: 4307 Cov.: 34

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0582

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.216 AC: 32904 AN: 152160 Hom.: 4309 Cov.: 34 AF XY: 0.213 AC XY: 15841 AN XY: 74378

African (AFR) AF: 0.361 AC: 14998 AN: 41510

American (AMR) AF: 0.240 AC: 3670 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3468

East Asian (EAS) AF: 0.109 AC: 565 AN: 5164

South Asian (SAS) AF: 0.0568 AC: 274 AN: 4828

European-Finnish (FIN) AF: 0.154 AC: 1633 AN: 10596

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10489 AN: 67974

Other (OTH) AF: 0.189 AC: 400 AN: 2112

Alfa AF: 0.195 Hom.: 411

Bravo AF: 0.232

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.0
DANN	Benign	0.75
PhyloP100		-4.7

Splicing

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

Other links and lift over

dbSNP: rs7279521; hg19: chr21-46405276;