rs77292666

Variant names:

• chr21-31841738-G-A
• rs77292666

Your query was ambiguous. Multiple possible variants found:

• chr21-31841738-G-A
• chr21-31841738-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 0.0259 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0522 AC: 2165 AN: 41452

American (AMR) AF: 0.0145 AC: 221 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0193 AC: 67 AN: 3466

East Asian (EAS) AF: 0.114 AC: 585 AN: 5132

South Asian (SAS) AF: 0.0314 AC: 151 AN: 4812

European-Finnish (FIN) AF: 0.00804 AC: 85 AN: 10576

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00898 AC: 610 AN: 67966

Other (OTH) AF: 0.0208 AC: 44 AN: 2114

Alfa AF: 0.00806 Hom.: 1

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
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs77292666; hg19: chr21-33214050;