rs208277

Variant names:

• chr12-121122778-C-T
• rs208277

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 0.596 in 151,794 control chromosomes in the GnomAD database, including 30,755 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 0.60 (30755 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.754 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: 0.597 AC: 90515 AN: 151674 Hom.: 30766 Cov.: 29

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.596 AC: 90506 AN: 151794 Hom.: 30755 Cov.: 29 AF XY: 0.599 AC XY: 44392 AN XY: 74170

African (AFR) AF: 0.247 AC: 10206 AN: 41352

American (AMR) AF: 0.766 AC: 11674 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2759 AN: 3468

East Asian (EAS) AF: 0.617 AC: 3168 AN: 5138

South Asian (SAS) AF: 0.612 AC: 2938 AN: 4802

European-Finnish (FIN) AF: 0.652 AC: 6854 AN: 10512

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.744 AC: 50541 AN: 67958

Other (OTH) AF: 0.664 AC: 1403 AN: 2112

Alfa AF: 0.716 Hom.: 67737

Bravo AF: 0.594

Asia WGS AF: 0.588 AC: 2047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.77
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs208277; hg19: chr12-121560581;