rs1861873

Variant names:

• chr12-14053667-A-G
• rs1861873

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 0.0625 in 152,258 control chromosomes in the GnomAD database, including 430 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 0.063 (430 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0987 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: 0.0626 AC: 9525 AN: 152140 Hom.: 429 Cov.: 32

Gnomad AFR AF: 0.0170

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.0494

Gnomad ASJ AF: 0.0544

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0675

Gnomad FIN AF: 0.0428

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0680

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

GnomAD4 genome AF: 0.0625 AC: 9521 AN: 152258 Hom.: 430 Cov.: 32 AF XY: 0.0596 AC XY: 4439 AN XY: 74454

African (AFR) AF: 0.0169 AC: 704 AN: 41580

American (AMR) AF: 0.0493 AC: 754 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0544 AC: 189 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5176

South Asian (SAS) AF: 0.0673 AC: 324 AN: 4814

European-Finnish (FIN) AF: 0.0428 AC: 454 AN: 10614

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6845 AN: 67990

Other (OTH) AF: 0.0673 AC: 142 AN: 2110

Alfa AF: 0.0568 Hom.: 126

Bravo AF: 0.0623

Asia WGS AF: 0.0220 AC: 76 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	0.12
DANN	Benign	0.59
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1861873; hg19: chr12-14206601;