chr21-31841738-G-A

Variant names:

• chr21-31841738-G-A
• rs77292666

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 0.0259 in 151,988 control chromosomes in the GnomAD database, including 97 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 0.026 (97 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.106 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: 0.0259 AC: 3935 AN: 151870 Hom.: 97 Cov.: 31

Gnomad AFR AF: 0.0523

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0145

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0314

Gnomad FIN AF: 0.00804

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00897

Gnomad OTH AF: 0.0196

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

GnomAD4 genome AF: 0.0259 AC: 3937 AN: 151988 Hom.: 97 Cov.: 31 AF XY: 0.0259 AC XY: 1927 AN XY: 74316

Gnomad4 AFR AF: 0.0522

Gnomad4 AMR AF: 0.0145

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.0314

Gnomad4 FIN AF: 0.00804

Gnomad4 NFE AF: 0.00898

Gnomad4 OTH AF: 0.0208

Alfa AF: 0.00580 Hom.: 0

Bravo AF: 0.0265

Asia WGS AF: 0.0640 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.097
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs77292666; hg19: chr21-33214050;