rs1571660

Variant names:

• chr21-25827185-G-A
• rs1571660

Your query was ambiguous. Multiple possible variants found:

• chr21-25827185-G-A
• chr21-25827185-G-C

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 0.507 in 151,990 control chromosomes in the GnomAD database, including 19,777 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 0.51 (19777 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.542 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: 0.507 AC: 77037 AN: 151872 Hom.: 19748 Cov.: 32

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.507 AC: 77106 AN: 151990 Hom.: 19777 Cov.: 32 AF XY: 0.510 AC XY: 37925 AN XY: 74318

African (AFR) AF: 0.513 AC: 21249 AN: 41444

American (AMR) AF: 0.528 AC: 8063 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1411 AN: 3466

East Asian (EAS) AF: 0.532 AC: 2745 AN: 5162

South Asian (SAS) AF: 0.559 AC: 2689 AN: 4808

European-Finnish (FIN) AF: 0.525 AC: 5536 AN: 10554

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33800 AN: 67958

Other (OTH) AF: 0.491 AC: 1038 AN: 2114

Alfa AF: 0.485 Hom.: 12761

Bravo AF: 0.509

Asia WGS AF: 0.561 AC: 1952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.66
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1571660; hg19: chr21-27199496; COSMIC: COSV53454588;