21-30260607-A-T

Variant names:

• chr21-30260607-A-T
• rs996610

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 0.841 in 152,128 control chromosomes in the GnomAD database, including 54,202 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 0.84 (54202 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 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: 0.841 AC: 127880 AN: 152010 Hom.: 54138 Cov.: 32

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.841 AC: 128002 AN: 152128 Hom.: 54202 Cov.: 32 AF XY: 0.841 AC XY: 62544 AN XY: 74368

African (AFR) AF: 0.938 AC: 38939 AN: 41530

American (AMR) AF: 0.839 AC: 12823 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2819 AN: 3472

East Asian (EAS) AF: 0.856 AC: 4420 AN: 5162

South Asian (SAS) AF: 0.883 AC: 4260 AN: 4824

European-Finnish (FIN) AF: 0.752 AC: 7946 AN: 10560

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53996 AN: 67976

Other (OTH) AF: 0.827 AC: 1749 AN: 2114

Alfa AF: 0.824 Hom.: 6444

Bravo AF: 0.850

Asia WGS AF: 0.872 AC: 3033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.28
DANN	Benign	0.43
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs996610; hg19: chr21-31632925;