rs200675

Variant names:

• chr21-23334400-A-G
• rs200675

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.706 in 152,066 control chromosomes in the GnomAD database, including 38,084 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 (38084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.738 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: 0.706 AC: 107250 AN: 151946 Hom.: 38052 Cov.: 32

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.706 AC: 107341 AN: 152066 Hom.: 38084 Cov.: 32 AF XY: 0.705 AC XY: 52411 AN XY: 74342

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.711

Alfa AF: 0.719 Hom.: 8015

Bravo AF: 0.707

Asia WGS AF: 0.738 AC: 2565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs200675; hg19: chr21-24706722;