rs1861693

Variant names:

• chr12-107209379-C-T
• rs1861693

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 0.216 in 152,120 control chromosomes in the GnomAD database, including 4,849 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 0.22 (4849 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 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: 0.215 AC: 32743 AN: 152002 Hom.: 4826 Cov.: 33

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.216 AC: 32820 AN: 152120 Hom.: 4849 Cov.: 33 AF XY: 0.215 AC XY: 15987 AN XY: 74370

African (AFR) AF: 0.410 AC: 17011 AN: 41472

American (AMR) AF: 0.225 AC: 3433 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 727 AN: 3470

East Asian (EAS) AF: 0.259 AC: 1341 AN: 5174

South Asian (SAS) AF: 0.174 AC: 839 AN: 4822

European-Finnish (FIN) AF: 0.121 AC: 1285 AN: 10596

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7453 AN: 67998

Other (OTH) AF: 0.200 AC: 422 AN: 2108

Alfa AF: 0.184 Hom.: 636

Bravo AF: 0.235

Asia WGS AF: 0.251 AC: 871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.55
DANN	Benign	0.49
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1861693; hg19: chr12-107603157;