rs821677

Variant names:

• chr10-106366383-C-T
• rs821677

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 0.863 in 152,172 control chromosomes in the GnomAD database, including 56,890 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 0.86 (56890 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 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: 0.863 AC: 131210 AN: 152052 Hom.: 56821 Cov.: 31

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.863 AC: 131336 AN: 152172 Hom.: 56890 Cov.: 31 AF XY: 0.861 AC XY: 64025 AN XY: 74396

African (AFR) AF: 0.940 AC: 39041 AN: 41526

American (AMR) AF: 0.860 AC: 13139 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2723 AN: 3472

East Asian (EAS) AF: 0.708 AC: 3654 AN: 5158

South Asian (SAS) AF: 0.832 AC: 4009 AN: 4816

European-Finnish (FIN) AF: 0.839 AC: 8894 AN: 10600

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57116 AN: 68008

Other (OTH) AF: 0.845 AC: 1781 AN: 2108

Alfa AF: 0.845 Hom.: 19492

Bravo AF: 0.868

Asia WGS AF: 0.783 AC: 2727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.041
DANN	Benign	0.51
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs821677; hg19: chr10-108126141;