rs1568050

Variant names:

• chr12-61397332-A-C
• rs1568050

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 0.0699 in 152,088 control chromosomes in the GnomAD database, including 1,090 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 0.070 (1090 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 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: 0.0699 AC: 10618 AN: 151970 Hom.: 1088 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.0326

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.0196

Gnomad SAS AF: 0.0457

Gnomad FIN AF: 0.000753

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00685

Gnomad OTH AF: 0.0556

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

GnomAD4 genome AF: 0.0699 AC: 10630 AN: 152088 Hom.: 1090 Cov.: 32 AF XY: 0.0686 AC XY: 5099 AN XY: 74324

African (AFR) AF: 0.221 AC: 9170 AN: 41472

American (AMR) AF: 0.0326 AC: 497 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 38 AN: 3470

East Asian (EAS) AF: 0.0193 AC: 100 AN: 5184

South Asian (SAS) AF: 0.0453 AC: 218 AN: 4812

European-Finnish (FIN) AF: 0.000753 AC: 8 AN: 10618

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00686 AC: 466 AN: 67974

Other (OTH) AF: 0.0550 AC: 116 AN: 2108

Alfa AF: 0.0522 Hom.: 93

Bravo AF: 0.0797

Asia WGS AF: 0.0380 AC: 134 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.3
DANN	Benign	0.66
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs1568050; hg19: chr12-61791113;