rs200675

Variant names:

• chr21-23334400-A-G
• rs200675

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 0.706 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.647 AC: 26821 AN: 41450

American (AMR) AF: 0.728 AC: 11131 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2444 AN: 3470

East Asian (EAS) AF: 0.670 AC: 3459 AN: 5166

South Asian (SAS) AF: 0.759 AC: 3661 AN: 4824

European-Finnish (FIN) AF: 0.718 AC: 7582 AN: 10560

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 49971 AN: 67988

Other (OTH) AF: 0.711 AC: 1504 AN: 2114

Alfa AF: 0.718 Hom.: 8175

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs200675; hg19: chr21-24706722;