rs12220777

Variant names:

• chr10-80028348-T-C
• rs12220777

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 0.107 in 152,030 control chromosomes in the GnomAD database, including 1,257 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 0.11 (1257 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.734
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 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: 0.107 AC: 16244 AN: 151912 Hom.: 1255 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.0698

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0838

Gnomad OTH AF: 0.0996

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

GnomAD4 genome AF: 0.107 AC: 16280 AN: 152030 Hom.: 1257 Cov.: 32 AF XY: 0.112 AC XY: 8343 AN XY: 74330

African (AFR) AF: 0.106 AC: 4401 AN: 41506

American (AMR) AF: 0.0698 AC: 1065 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0922 AC: 319 AN: 3458

East Asian (EAS) AF: 0.396 AC: 2046 AN: 5170

South Asian (SAS) AF: 0.224 AC: 1078 AN: 4820

European-Finnish (FIN) AF: 0.126 AC: 1334 AN: 10592

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0838 AC: 5698 AN: 67974

Other (OTH) AF: 0.102 AC: 215 AN: 2100

Alfa AF: 0.0887 Hom.: 1698

Bravo AF: 0.103

Asia WGS AF: 0.289 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	15
DANN	Benign	0.96
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs12220777; hg19: chr10-81788104;